Novel full spectrum anti-dengue antibody

ABSTRACT

The present invention provides, among other things, antibody agents (e.g., antibodies, and/or antigen-binding fragments thereof) that bind to DV epitopes, as well as compositions containing them and methods of designing, providing, formulating, using, identifying and/or characterizing them. In some embodiments, provided antibody agents show significant binding to a plurality of DV serotypes. In some embodiments, provided antibody agents show significant binding to all four DV serotypes. Such antibody agents are useful, for example, in the prophylaxis, treatment, diagnosis, and/or study of DV.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Division of application Ser. No. 15/868,328, filedon Jan. 11, 2018, issued as U.S. Pat. No. 10,519,220, which is aDivision of application Ser. No. 14/620,144, filed on Feb. 11, 2015,issued as U.S. Pat. No. 9,902,764, which claims priority to U.S.Provisional Patent Application Ser. No. 61/938,605, filed Feb. 11, 2014;the entirety of which is hereby incorporated by reference.

GOVERNMENT SUPPORT

This invention was made with government support under Grant No. R37GM057073 awarded by the National Institutes of Health (NIH). TheGovernment has certain rights in the invention.

SEQUENCE LISTING

The present specification makes reference to a Sequence Listing(submitted electronically as a .txt file named “Sequence Listing.txt” onFeb. 11, 2014). The .txt file was generated on Feb. 11, 2014 and is 19kb in size. The entire contents of the Sequence Listing are hereinincorporated by reference.

BACKGROUND

Dengue virus (DV) is a member of the virus family Falviviridae and istransmitted to people by several species of mosquito within the genusAedes, principally Aedes aegypti. Over 3.6 billion people worldwide areat risk of being infected with DV and more than 200 million infectionsof DV are estimated to occur each year globally (McBride et al., 2000Microbes & Infection 2:1041-1050, Guzman et al., 2010 Nature Rev.Microbiol. 8:S7-16). Dengue Fever is the most medically relevantarboviral disease in humans. The significant increases in incidence,geographical outreach, and severity of disease cases of Dengue aremaking DV a major human pathogen. Unfortunately, effective therapeuticregimens are not currently available; the most effective currentprevention measures lie in mosquito control.

SUMMARY

The present invention provides methods and compositions for thetreatment and/or prevention of DV infection. Among other things, thepresent invention provides antibody agents that neutralize all four DVserotypes. In some embodiments, provided antibody agents are variants ofreference antibody 4E11; in some such embodiments, provided antibodyagents have amino acid sequences that show high overall sequenceidentity with that of 4E11, or a relevant fragment thereof, yet includespecific sequence variations as compared with 4E11. In some embodiments,provided antibody agents show a significant improvement inneutralization of at least one DV serotype as compared with thatobserved for 4E11.

The present invention provides the insight that reference antibody 4E11,has certain desirable attributes, including binding to all four DVserotypes and having potent neutralizing ability of three of the four DVserotypes, but also lacks the ability to effectively neutralize thefourth DV serotype. The present invention identifies the source of theproblem of 4E11's inability to effectively neutralize this fourth DVserotype. In particular, the present invention defines structuralfeature modifications that improve the ability of an antibody agentwhose sequence contains the modification(s) to neutralize the relevantDV serotype, as compared with the ability of 4E11, which lacks themodifications. The present invention therefore defines and providesantibodies having structures that include the relevant structuralfeature modifications (but may otherwise be substantially identical tothat of 4E11) and being characterized by an ability to neutralize DVserotype 4 (DV4). In some embodiments, provided antibody agents showabilities to neutralize each of the other three DV serotypes that arenot significantly reduced as compared that of 4E11. Indeed, in someembodiments, provided antibody agents are characterized by a surprisingincrease in neutralization capability with respect to one or more of theother three DV serotypes (DV1-4) as compared with that observed with4E11.

In some embodiments, provided antibody agents are variants of referenceantibody 4E5A; in some such embodiments, provided antibody agents haveamino acid sequences that show high overall sequence identity with thatof 4E5A, or a relevant fragment thereof, yet include specific sequencevariations as compared with 4E5A. In some embodiments, provided antibodyagents show a significant improvement in neutralization of at least oneDV serotype as compared with that observed for 4E5A.

The present invention provides the insight that reference antibody 4E5A,has certain desirable attributes, including binding to all four DVserotypes and significant neutralizing ability of all four DV serotypes,but still shows low relative neutralizing ability with respect to DV4.For example, the present invention encompasses the recognition thatreference antibody 4E5A shows a KD with respect to D4 that is almostfive times its KD for DV3, and more than 500 times its KD for DV1.

The present invention identifies the source of the problem of 4E5A's lowrelative affinity for this fourth DV serotype. In particular, thepresent invention defines structural feature modifications that improvethe ability of an antibody agent whose sequence contains themodification(s) to neutralize the relevant DV serotype, as compared withthe ability of 4E5A, which lacks the modifications. The presentinvention therefore defines and provides antibody agents havingstructures that include the relevant structural feature modifications(but may otherwise be substantially identical to that of 4E5A and/or of4E11) and being characterized by one or more of: (i) KD below about 100nM for each of DV1, DV2, DV3, and DV4; (ii) KD relative to 4E5A for DV4greater than 1.25; (iii) KD for DV4 (relative to 4E5A) that is not lessthan 1.75 times the KD for DV3 relative to 4E5A; (iv) KD for DV4 atleast 2.1 times the KD for DV3.

In some embodiments, provided antibody agents show abilities toneutralize each of the other three DV serotypes that are notsignificantly reduced as compared that of 4E5A. In some embodiments,provided antibody agents show abilities to neutralize each of the otherthree DV serotypes that are not significantly reduced as compared thatof both 4E5A and 4E11. Indeed, in some embodiments, provided antibodyagents are characterized by a surprising increase in neutralizationcapability with respect to one or more of the other three DV serotypes(DV1-4) as compared with that observed with 4E5A. In some embodiments,provided antibody agents are characterized by a surprising increase inneutralization capability with respect to one or more of the other threeDV serotypes (DV1-4) as compared with that observed with both 4E5A and4E11. The present invention provides technologies for definingstructural modifications that impart biological activities of interestto polypeptides, while maintaining structural features required topreserve other activities.

In some embodiments, the present invention provides antibody agents thatbind to DV epitopes, as well as compositions containing them and methodsof designing, providing, formulating, using, identifying and/orcharacterizing them. In some embodiments, provided antibody agents showsignificant binding to a plurality of DV serotypes. In some embodiments,provided antibody agents show significant binding to all four DVserotypes. Provided antibody agents are useful, for example, in theprophylaxis, treatment, diagnosis, and/or study of DV.

In some embodiments, provided antibody agents cross-compete with one ormore previously-described reference anti-DV antibodies. In someembodiments, provided antibody agents bind to an epitope that is orcomprises an amino acid sequence within SEQ ID NO. 17 (EDIII-DV1), SEQID NO. 18 (EDIII-DV2), SEQ ID NO. 19 (EDIII-DV3), SEQ ID NO. 20(EDIII-DV4) and/or combinations thereof. In some embodiments, providedantibody agents do not significantly cross-compete with one or moreparticular previously-described anti-DV antibodies.

In some embodiments, provided antibody agents neutralize DV inestablished model systems with greater potency with respect to at leastone (e.g., with respect to one, two, three, or four) DV serotype thandoes one or more previously-described reference anti-DV antibodies. Insome embodiments, provided antibody agents neutralize DV in establishedmodel systems with greater potency with respect to all four DV serotypesthan does one or more previously-described reference anti-DV antibodies.In some embodiments, provided antibody agents neutralize DV inestablished model systems with increased comparability of relativepotencies as compared with one or more reference anti-DV antibodies(e.g., 4E11 and/or 4E5A). The present invention encompasses, among otherthings, the recognition that provided antibody agents may offer greatertherapeutic and/or prophylactic benefit than do previously-describedanti-DV antibodies.

Provided antibody agents are useful in a variety of contexts including,for example, in therapeutic, prophylactic, diagnostic, and/or researchapplications. In some embodiments, provided antibody agents are usefulin the treatment of chronic and/or acute DV infection, for example byadministering to a subject suffering from or susceptible to suchinfection a therapeutically effective amount of one or more providedsuch provided antibody agents. In some embodiments, a therapeuticallyeffective amount is an amount sufficient to achieve one or moreparticular biological effects, including, but not limited to, (i)reducing severity or frequency of, and/or delaying onset or re-emergenceof one or more symptoms or characteristics of DV infection in anindividual susceptible to or suffering from DV infection; and/or (ii)reducing risk of infection and/or of development of one or more symptomsor characteristics of DV infection in an individual exposed or at riskof exposure to DV infection. In some embodiments, the one or moresymptoms or characteristics of DV infection is or comprises high feverand at least one or more additional symptoms selected for example fromsevere headache, severe eye pain, joint pain, muscle pain, bone pain,rash, mild bleeding manifestation (e.g., nose or gum bleeding,petechiae, easy bruising), abdominal pain, vomiting, black, tarrystools, drowsiness or irritability, pale, cold or clammy skin,difficulty breathing, low white cell count, circulating viral particlesin an individual or one or more tissues (e.g., blood, bone marrow) ororgans (e.g., liver) thereof. In some embodiments, an individualsuffering from DV infection displays high fever and at least two suchadditional symptoms.

In some embodiments, provided antibody agents may be used to prevent,reduce recurrence of, and/or delay onset of one or more symptoms orcharacteristics of DV infection. In some embodiments, provided antibodyagents may be used, for example, for passive immunization of individualsrecently exposed to DV or at risk of being exposed to DV, newborn babiesborn to DV-positive mothers, and/or liver transplantation patients(e.g., to prevent possible recurrent DV infections in such patients).

In some embodiments, the present invention provides viral mimic agentswhose structure includes one or more conserved elements of certain DVantigens, for example sufficient to permit the viral mimic agent tomimic one or more biological activities of the relevant DV antigen. Insome embodiments, such viral mimic agents include such conservedstructural elements of DV antigens, for example as defined herein, andlack one or more other structural elements of the DV antigens. In someembodiments, provided viral mimic agents are or comprise one or morepolypeptides. In some embodiments, provided viral mimic agentpolypeptides have amino acid sequences that include one or moreconserved sequence elements from a DV antigen; in some embodiments,provided viral mimic agent polypeptides lack one or more other sequenceelements from the DV antigen. For example, in some embodiments, providedviral mimic agent polypeptides are or comprise fragments of a DVantigen.

In some embodiments, the present invention provides therapeutic methodsof treatment, utilized after development of one or more symptoms of DVinfection. In some embodiments, the present invention providestherapeutic methods of prophylaxis, utilized prior to development of oneor more symptoms of DV infection, and/or prior to exposure to DV, DVinfection, or risk thereof. In some particular embodiments, the presentinvention provides passive immunization technologies.

In some embodiments, the present invention provides diagnostic methodsof detecting DV in and/or otherwise characterizing samples such asclinical, environmental, and/or research samples.

The present invention provides systems for designing, identifying,and/or characterizing useful anti-DV antibody agents. For example, insome embodiments, the present invention provides empirical computationalapproaches that capture particular physicochemical features common toprotein interfaces. In some embodiments, such approaches permitprediction of protein-protein interactions (e.g., antigen-antibodyinteractions), including for example predicting which amino acidsequences might show particularly high interaction affinity. In someembodiments, provided approaches are usefully applied to design,identify, and/or characterize sequences that differ from a referencesequence and show one or more improved characteristics (e.g., improvedaffinity) with regard to their protein-protein interactions.

The present invention provides systems for stratifying patients based ontheir immunological response to DV. The present invention providesmethods for identifying those patients likely to respond well to DVimmunotherapy. For example, a patient's serum may be used to test forthe presence of antibodies directed against a particular epitope of DV(e.g., epitope to which provided antibody agents specifically binds). Ifthe patient does not have adequate levels of antibodies directed to suchan epitope, one or more provided DV antibody agents may be administeredto the patient. The patient's own immune response may be supplementedwith provided DV antibody agents. In some embodiments, immunotherapyaids in clearance of DV virus and/or resolution of DV infection. In someembodiments, immunotherapy in accordance with the present inventiontreats and/or prevents chronic DV infection.

In some embodiments, the present invention provides methods ofdesigning, identifying and/or characterizing useful antibody agents. Forexample, in some embodiments, such methods involve determining whether atest antibody agent competes for antigen binding with one or morereference anti-DV antibodies and/or other antibody agents. In someembodiments, a test antibody agent is identified as a useful antibodyagent if it cross-competes with one or more reference DV antibodies.

In some embodiments, provided antibody agents are combined with one ormore additional pharmaceutically acceptable substances to providepharmaceutical compositions. The present invention providespharmaceutical compositions for treatment, prevention, diagnosis and/orcharacterization of DV infection.

In some embodiments, pharmaceutical compositions comprise antibodyagents that are or comprise, for example, human antibodies or fragmentsor variants thereof that bind to any DV serotype and neutralize DVinfection in vitro. In some embodiments, pharmaceutical compositionscomprise antibody agents that are or comprise, for example humanantibodies or fragments or variants thereof that bind to any DV serotypeand neutralize DV infection in vivo. In some embodiments, DVneutralization by provided antibody agents in in vitro systems iscorrelative and/or predictive of DV neutralization by provided antibodyagents in vivo (e.g., in humans and/or other mammals).

In some embodiments, provided antibody agents may be utilized togetherwith one or more other therapies for treating, reducing incidence,frequency, or severity of, and/or delaying onset of DV infection or oneor more symptoms or characteristics thereof. For example, in someembodiments, provided antibody agents are utilized together with one ormore anti-viral agents, anti-inflammatories, pain relievers,immunomodulating therapeutics and combination therapy, which preferablyinvolves other DV targets. For example, in some embodiments, in someembodiments, provided antibody agents are administered in combinationwith one or more interferons (e.g., interferon α-2b, interferon-γ,etc.), analgesics (preferably containing acetaminophen and not aspirinand/or ibuprofen), anti-DV monoclonal antibodies, anti-DV polyclonalantibodies, RNA polymerase inhibitors, protease inhibitors, nucleosideanalogs, helicase inhibitors, immunomodulators, antisense compounds,short interfering RNAs (siRNAs), short hairpin RNAs (shRNAs), micro RNAs(miRNAs), RNA aptamers, ribozymes, and combinations thereof.

Thus, in some embodiments, the invention specifically provides anantibody agent which binds to and neutralizes each of Dengue Virusserotypes D1, D2, D3, and D4. In some embodiments, the antibody agentbinds to an epitope that is or comprises an amino acid sequence within:SEQ ID NO. 17 (EDIII-DV1), SEQ ID NO. 18 (EDIII-DV2), SEQ ID NO. 19(EDIII-DV3), SEQ ID NO. 20 (EDIII-DV4), or combinations thereof. In someembodiments, the antibody agent binds to an epitope in the A-strandregion of envelop glycoprotein of Dengue virus.

In some embodiments, the epitope comprises one or more residuescorresponding to that at a position selected from the group consistingof 305, 306, 307, 308, 309, 310, 311, 312, 323, 325, 327, 329, 360, 361,362, 363, 364, 385, 387, 388, 389, 390, 391, and combinations thereof,of any one of SEQ ID NOs. 17-20. In some embodiments, the correspondingresidue at position 305 is selected from the group consisting of:serine, lysine, and threonine. In some embodiments, the correspondingresidue at position 310 is lysine. In some embodiments, thecorresponding residue at position 311 is lysine. In some embodiments,the corresponding residue at position 323 is selected from the groupconsisting of arginine, lysine, and glutamine. In some embodiments, thecorresponding residue at position 327 is selected from the groupconsisting of lysine and glutamate. In some embodiments, thecorresponding residue at position 329 is selected from the groupconsisting of arginine, aspartate, glutamate, and threonine.

In some embodiments, the invention provides an antibody agent whoseheavy chain variable region and/or light chain variable region includesat least one complementarity determining region (CDR) sharing at least80% sequence identity with a CDR of reference antibody 4E11, but differsby substitution of at least one amino residue within the CDR. In someembodiments, the invention provides an antibody agent whose heavy chainvariable region and/or light chain variable region includes at least onecomplementarity determining region (CDR) sharing at least 80% sequenceidentity with a CDR of reference antibody 4E5A, but differs bysubstitution of at least one amino residue within the CDR. In someembodiments, one or more such substitution(s) is/are a homologoussubstitution(s). In some embodiments, one or more such substitution(s)is/are not a homologous substitution(s). In some embodiments, one ormore such substitutions is/are a null substitution(s).

In some embodiments, the antibody agent includes at least one CDR thatis substantially identical to a reference CDR of antibody 4E11 in thatit is either identical to such reference CDR or includes between 1-5substitutions of amino acids within such reference CDR. In someembodiments, the reference CDR is selected from the group consisting ofone found between residues 27 and 33 of the 4E11 heavy chain (SEQ ID NO.1), one found between residues 53 and 58 of the 4E11 heavy chain (SEQ IDNO. 1), one found between residues 100 and 106 of the 4E11 heavy chain(SEQ ID NO. 1), one found between residues 24 and 38 of the 4E11 lightchain (SEQ ID NO. 2), one found between residues 54 and 60 of the 4E11light chain (SEQ ID NO. 2), one found between residues 93 and 101 of the4E11 light chain (SEQ ID NO. 2); and combinations thereof. In someembodiments, the antibody agent includes at least one CDR that issubstantially identical to a reference CDR set forth below, in that itis either identical to such reference CDR or includes between 1-5substitutions of amino acids within such reference CDR: GFNIKDT (SEQ IDNO. 7), DPANGD (SEQ ID NO. 8), GWEGFAY (SEQ ID NO. 9), RASENVDKYGNSFMH(SEQ ID NO. 14), RASNLES (SEQ ID NO. 15), and/or QRSNEVPWT (SEQ ID NO.16). In some embodiments, the reference CDR is a heavy chain CDR. Insome embodiments, the reference CDR is a light chain CDR. In someembodiments, the antibody agent includes at least one heavy chain CDRthat is substantially identical to a heavy chain reference CDR and alsoincludes at least one light chain CDR that is identical to a light chainreference CDR. In some embodiments, each of the CDRs in the antibodyagent is substantially identical to one of the reference CDRs.

In some embodiments, the invention provides an antibody agent whoseheavy chain variable region includes at least one complementaritydetermining region (CDR) sharing at least 95% sequence identity with aCDR of reference antibody 4E11, but differs by substitution of at leastone amino acid residue within the CDR. In some embodiments, the antibodyagent includes at least one CDR that is substantially identical to areference CDR of antibody 4E11 in that it is either identical to suchreference CDR or includes between 1-5 substitutions of amino acidswithin such reference CDR. In some embodiments, the reference CDR isselected from the group consisting of one found between residues 27 and33 of the 4E11 heavy chain (SEQ ID NO. 1), one found between residues 53and 58 of the 4E11 heavy chain (SEQ ID NO. 1), one found betweenresidues 100 and 106 of the 4E11 heavy chain (SEQ ID NO. 1), one foundbetween residues 24 and 38 of the 4E11 light chain (SEQ ID NO. 2), onefound between residues 54 and 60 of the 4E11 light chain (SEQ ID NO. 2),one found between residues 93 and 101 of the 4E11 light chain (SEQ IDNO. 2), and combinations thereof. In some embodiments, the antibodyagent includes at least one CDR that is substantially identical to areference CDR set forth below, in that it is either identical to suchreference CDR or includes between 1-5 substitutions of amino acidswithin such reference CDR reference CDRs: GFNIKDT (SEQ ID NO. 7), DPANGD(SEQ ID NO. 8), GWEGFAY (SEQ ID NO. 9), RASENVDKYGNSFMH (SEQ ID NO. 14),RASNLES (SEQ ID NO. 15), and/or QRSNEVPWT (SEQ ID NO. 16). In someembodiments, the reference CDR is a heavy chain CDR. In someembodiments, the reference CDR is a light chain CDR. In someembodiments, the antibody agent includes at least one heavy chain CDRthat is substantially identical to a heavy chain reference CDR and alsoincludes at least one light chain CDR that is identical to a light chainreference CDR. In some embodiments, each of the CDRs in the antibodyagent is substantially identical to one of the reference CDRs. In someembodiments, the heavy chain variable region CDR has substitution of theamino acid residue at position 55. In some embodiments, the substituteamino acid at position 55 is selected form the group consisting ofglutamate and aspartate. In some embodiments, the light chain variableregion CDR has substitution of the amino acid residue at positionsselected from the group consisting of 27, 31, 57, 59, 60, andcombinations thereof. In some embodiments, the substitute amino acidresidue at position 27 is a null substitute (i.e., a deletion of asingle amino acid). In some embodiments, the substitute amino acidresidue at position 27 is alanine. In some embodiments, the substituteamino acid residue at position 31 is lysine. In some embodiments, thesubstitute amino acid residue at position 57 is selected from the groupconsisting of glutamate and serine. In some embodiments, the substituteamino acid residue at position 59 is selected from the group consistingof glutamine and asparagine. In some embodiments, the substitute aminoacid residue at position 60 is selected from the group consisting oftryptophan, tyrosine, and arginine.

In some embodiments, the antibody agent includes at least one CDR thatis substantially identical to a reference CDR of antibody 4E5A in thatit is either identical to such reference CDR or includes between 1-5substitutions of amino acids within such reference CDR. In someembodiments, the reference CDR is selected from the group consisting ofone found between residues 27 and 33 of the 4E5A heavy chain (SEQ ID NO.29), one found between residues 53 and 58 of the 4E5A heavy chain (SEQID NO. 29), one found between residues 100 and 106 of the 4E5A heavychain (SEQ ID NO. 29), one found between residues 24 and 38 of the 4E5Alight chain (SEQ ID NO. 30), one found between residues 54 and 60 of the4E5A light chain (SEQ ID NO. 30), one found between residues 93 and 101of the 4E5A light chain (SEQ ID NO. 30); and combinations thereof. Insome embodiments, the antibody agent includes at least one CDR that issubstantially identical to a reference CDR set forth below, in that itis either identical to such reference CDR or includes between 1-5substitutions of amino acids within such reference CDR: GFNIKDT (SEQ IDNO. 35), DPENGD (SEQ ID NO. 36), GWEGFAY (SEQ ID NO. 37),RASENVDKYGNSFMH (SEQ ID NO. 42), RASELQW (SEQ ID NO. 3), and/orQRSNEVPWT (SEQ ID NO. 44). In some embodiments, the reference CDR is aheavy chain CDR. In some embodiments, the reference CDR is a light chainCDR. In some embodiments, the antibody agent includes at least one heavychain CDR that is substantially identical to a heavy chain reference CDRand also includes at least one light chain CDR that is identical to alight chain reference CDR. In some embodiments, each of the CDRs in theantibody agent is substantially identical to one of the reference CDRs.

In some embodiments, the invention provides an antibody agent whoseheavy chain variable region includes at least one complementaritydetermining region (CDR) sharing at least 95% sequence identity with aCDR of reference antibody 4E5A, but differs by substitution of at leastone amino acid residue within the CDR. In some embodiments, the antibodyagent includes at least one CDR that is substantially identical to areference CDR of antibody 4E5A in that it is either identical to suchreference CDR or includes between 1-5 substitutions of amino acidswithin such reference CDR. In some embodiments, the reference CDR isselected from the group consisting of one found between residues 27 and33 of the 4E5A heavy chain (SEQ ID NO. 29), one found between residues53 and 58 of the 4E5A heavy chain (SEQ ID NO. 29), one found betweenresidues 100 and 106 of the 4E5A heavy chain (SEQ ID NO. 29), one foundbetween residues 24 and 38 of the 4E5A light chain (SEQ ID NO. 30), onefound between residues 54 and 60 of the 4E5A light chain (SEQ ID NO.30), one found between residues 93 and 101 of the 4E5A light chain (SEQID NO. 30), and combinations thereof. In some embodiments, the antibodyagent includes at least one CDR that is substantially identical to areference CDR set forth below, in that it is either identical to suchreference CDR or includes between 1-5 substitutions of amino acidswithin such reference CDR: GFNIKDT (SEQ ID NO. 35), DPENGD (SEQ ID NO.36), GWEGFAY (SEQ ID NO. 37), RASENVDKYGNSFMH (SEQ ID NO. 42), RASELQW(SEQ ID NO. 3), and/or QRSNEVPWT (SEQ ID NO. 44). In some embodiments,the reference CDR is a heavy chain CDR. In some embodiments, thereference CDR is a light chain CDR. In some embodiments, the antibodyagent includes at least one heavy chain CDR that is substantiallyidentical to a heavy chain reference CDR and also includes at least onelight chain CDR that is identical to a light chain reference CDR. Insome embodiments, each of the CDRs in the antibody agent issubstantially identical to one of the reference CDRs.

In some embodiments, the present invention provides an antibody agentwhose amino acid sequence includes a portion showing substantialidentity to a corresponding portion of a reference antibody sequence(e.g., found in a heavy or light chain of antibody 4E11 and/or 4E5A),but for precise differences at a small number of positions. In someembodiments, the portion includes a sequence adjacent a CDR; in someembodiments, the portion includes a CDR; in some embodiments, theportion includes 1, 2, or 3 CDRs; in some embodiments, the portioncorresponds to a full-length chain. In some embodiments, the portion isat least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 50 or more amino acids in length. In some embodiments, the providedantibody agent shows at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greatersequence identity with the reference sequence across the portion.

In some embodiments, the present invention provides an antibody agentcomprising a polypeptide includes one or more of the following CDRsequences:

(SEQ ID NO. 35) GFNIKDT, (SEQ ID NO. 36) DPENGD, (SEQ ID NO. 37)GWEGFAY, (SEQ ID NO. 42) RASENVDKYGNSFMH, (SEQ ID NO. 3) RASELQW, and/or(SEQ ID NO. 44) QRSNEVPWT.

In some embodiments, the present invention provides an antibody agentcomprising at least first and second polypeptides, each of whichincludes one or more of these CDR sequences. In some embodiments, thepresent invention provides an antibody agent comprising at least first,second and third polypeptides, each of which includes one or more ofthese CDR sequences. In some embodiments, the present invention providesan antibody agent comprising at least first, second and thirdpolypeptides, each of which includes one or more of these CDR sequencesand framework regions, each of which includes one of more of thefollowing sequences: EVKLLEQSGAELVKPGASVRLSCTAS (SEQ ID NO. 31),YMSWVKQRPEQGLEWIGRI (SEQ ID NO. 32),TKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYCSR (SEQ ID NO. 33), and/orWGQGTLVTVSA (SEQ ID NO. 34). In some embodiments, the present inventionprovides an antibody agent which is a full antibody comprisingpolypeptides that include a heavy chain of sequence SEQ ID NO. 29 and alight chain of sequence SEQ ID NO. 30.

In some embodiments, the present invention provides an antibody agentcomprising a polypeptide whose amino acid sequence includes a portioncorresponding to a fragment of a reference 4E11 or 4E5A heavy chain thatincludes residues 26 and/or 27. In some such embodiments, the providedantibody agent has an amino acid sequence that differs from that of thereference at one or both of positions 26 and 27. In some embodiments,the present invention provides antibody agents that have a nullsubstitution (i.e. deletion) of the amino acid residue at position 26relative to the reference polypeptide. In some embodiments, the presentinvention provides antibody agents that have a null substitution (i.e.deletion) of the amino acid residue at position 27 relative to thereference polypeptide. In some embodiments, the present inventionprovides antibody agents that have a substitution of the amino acidresidue at position 27 relative to the reference polypeptide. In someembodiments, the substitute amino acid residue at position 27 isalanine.

In some embodiments, the present invention provides an antibody agentcomprising a polypeptide whose amino acid sequence shows at least 80%identity to that of a reference 4E11 or 4E5A heavy chain or light chain,which at least one polypeptide includes the following sequence elements:

Null at heavy chain residue 26

A at heavy chain residue 27

Null at heavy chain residue 27.

In some embodiments, the present invention provides an antibody agentcomprising a polypeptide whose amino acid sequence that is identical tothat of a reference 4E11 or 4E5A heavy chain or light chain, except thatit differs in at least one position, but not in more than 10, 9, 8, 7,6, 5, 4, 3, or 2 positions, which at least one polypeptide includes thefollowing sequence elements:

Null at heavy chain residue 26

A at heavy chain residue 27

Null at heavy chain residue 27.

In some embodiments, the invention provides an antibody agent which isan IgG. In some embodiments, an antibody agent is a monoclonal antibody.In some embodiments, an antibody agent is selected from the groupconsisting of: a mouse antibody, a humanized antibody, a human antibody,a purified antibody, an isolated antibody, a chimeric antibody, apolyclonal antibody, and combinations thereof. In some embodiments, anantibody agent is provided wherein the antigen binding fragment isselected from the group consisting of: a Fab fragment, a Fab′ fragment,a F(ab′)2 fragment, a Fd fragment, a Fd′ fragment, a Fv fragment, a dAbfragment, a scFv fragment, an isolated CDR region, a dsFv diabody, asingle chain antibody, and combinations thereof.

In some embodiments, the invention provides a cell line expressing anantibody agent specific to Dengue virus, wherein the antibody agentbinds to and neutralizes each of Dengue Virus serotypes D1, D2, D3, andD4. In some embodiments, the invention provides a pharmaceuticalcomposition including one or more antibody agents wherein the antibodyagent binds to and neutralizes each of Dengue Virus serotypes D1, D2,D3, and D4 and a pharmaceutically acceptable excipient. In someembodiments, a pharmaceutical composition further includes at least oneadditional antiviral agent.

In some embodiments, the invention provides methods of treating asubject in need thereof, including the step of administering an antibodyagent wherein the antibody agent binds to and neutralizes each of DengueVirus serotypes D1, D2, D3, and D4. In some embodiments, the inventionprovides kits including at least one antibody agent wherein the antibodyagent binds to and neutralizes each of Dengue Virus serotypes D1, D2,D3, and D4, a syringe, needle, or applicator for administration of theat least one antibody or fragment to a subject, and instructions foruse.

In some embodiments, the invention provides methods of manufacturingpharmaceutical compositions, the method including the steps of providingan antibody agent wherein the antibody agent binds to and neutralizeseach of Dengue Virus serotypes D1, D2, D3, and D4, and formulating theantibody agent with at least one pharmaceutically acceptable carrier, sothat a pharmaceutical composition is generated. In some embodiments, thepharmaceutical composition is a liquid composition. In some embodiments,the pharmaceutical composition is formulated for parenteraladministration. In some embodiments, the pharmaceutical composition isformulated for intravenous administration. In some embodiments, thepharmaceutical composition is formulated for intravenous administrationto a child.

BRIEF DESCRIPTION OF THE DRAWING

The Figures of the Drawing are for illustration purposes only, not forlimitation.

FIG. 1: FIG. 1 shows the effect of window size on prediction accuracy.The window size represents the number of predicted positives. Predictionaccuracy is determined by the number of test case structures (overall37) correctly predicted. When the window size is one (i.e., when one outof 101 structures is predicted to be positive), nearly half of the x-raystructures (48%˜18 out of 37) were correctly identified, the binomialprobability of which is 1.46E-26 (n=37, p=0.009, number of successes=18)if the structures were chosen at random. The prediction accuracy ofMLR-method is seen to be a logarithmically increasing function of windowsize with accuracy reaching 85% at window size 5 and 100% at window size10. On the contrary, ZRANK fails to predict 100% of the structures evenwhen the window size is 20.

FIG. 2A, FIG. 2B, and FIG. 2C: illustrate docking results of a localsearch. For this assessment, native-like structures are defined ashaving less that 3 angstroms (Å) RMSD from the ligand in the x-raystructure, calculated for ligand atoms that are within 7 Å of the fixedreceptor. Structures that have RMSD>3 Å are referred to as non-nativestructures. (A) Each point on the surface plot represents a dockingdecoy. The x-axis shows the ZRANK score; the Y-axis represents RMSD (inÅ) to the X-ray structure; the Z axis represents MLR based predictionprobabilities. ZRANK scores of native-like structures vary between −60to −30 Kcal/mol. (B) Correlation between ZRANK scores (x-axis) and RMSD(y-axis). Data points inside dotted circles are close to native x-raystructure. (C) Correlation between MLR-based probability and RMSD. Thereis a significant correlation between prediction probabilities vs. RMSDbut no such correlation exists between ZRANK and RMSD.

FIG. 3: FIG. 3 demonstrates the affinity and in vitro activity of 4E11antibody.

FIG. 4: FIG. 4 shows a flowchart of the antibody design approach.

FIG. 5: FIG. 5 demonstrates the superposition of the top five dockingmodels on fixed EDIII. EDIII domain is represented as spheres; 4E11,displayed as the surface in each model.

FIG. 6A AND FIG. 6B: illustrate sequence and structural determinants ofpoor DV4 binding. (A) Sequence alignment of EDIII domain region of fourserotypes. Putative mAb binding residues are shaded in grey. Residues at307, 329, 361, 364, 385, 388 and 390 differentiate DV4 from reminder ofthe sequences; these are numbered. Residue contacts made by the five mAbmutations are boxed. Notably, 5 out of 6 new contacts are formed againstconserved epitope residues of A & B strands. This explains why the newmutations are not detrimental to DV1-3 binding. (B) Structural model of4E11/EDIII interaction. Sequence positions that discriminate DV4 fromother strains are labeled and the side chains of amino acids thereinrepresented as sticks.

FIG. 7: FIG. 7 demonstrates that affinity-enhancing mutations localizeto the periphery of the 4E11:EDIII-DV4 interface. The positive positionsidentified in the binding screen are highlighted and shown in astructural model of 4E11:EDIII-DV4 interaction. All positive mutationsare located at the periphery of the binding interface. The two panelsrepresent different views of the same model. EDIII (top), VH (right),and VL (left) proteins are represented respectively, in each panel.

FIGS. 8A-D and FIGS. 8E-H: show surface plasmon resonance (SPR)sensograms of 4E11 WT and 4E5A with antigens EDIII of DV1-4. (FIG. 8A)4E11:EDIII-DV1; (FIG. 8B) 4E11:EDIII-DV2; (FIG. 8C) 4E11:EDIII-DV3;(FIG. 8D) 4E11:EDIII-DV4; (FIG. 8E) 4E5A:EDIII-DV1; (FIG. 8F)4E5A:EDIII-DV2; (FIG. 8G) 4E5A:EDIII-DV3; and (FIG. 8H) 4E5A:EDIII-DV4.

FIG. 9: FIG. 9 illustrates in vitro neutralizing activity of antibodiesassessed by focus reduction neutralization test (FRNT). Neutralizationassays were performed with DV1-4 and antibodies 4E11 WT, m4E11 WT, 4E5A,and 4G2. Serial dilutions of antibody were mixed with equal amounts ofvirus and added to Vero cell monolayers with a viscous overlay. After4-6 days, cells were fixed and foci were immunostained and counted. Datapoints represent averages of duplicates with error bars representingstandard deviation. A standard four-parameter logistic model was fit tothe data using least squares regression. 4E5A shows similar neutralizingactivity to 4E11 and m4E11 for DV1-3 and a substantial increase inneutralizing activity to DV4. 4G2, a representative flavivirusfusion-loop specific antibody, demonstrates lower neutralizing activityfor DV1-3 and only slightly higher activity to DV4 relative to 4E5A.

FIG. 10: FIG. 10 shows in vivo prophylactic DV2 challenge model. Thedata show virus in the serum of AF129 mice on day 3 after viruschallenge. Mice treated with AB1 or placebo 1 day prior to viruschallenge. RNA extracted from the serum of the mice was amplified byQRT-PCR and an approximate Log₁₀CCID₅₀ titer was extrapolated based on acurve from control RNA taken from a sample of known titer. The dashedline represents the approximate limit of detection.

FIG. 11: FIG. 11 demonstrates amino acid frequencies in paratope andepitope. Data generated from 77 antigen-antibody complexes.

FIG. 12: FIG. 12 demonstrates the affinity of 4E5A antibody variants forEDIII-DVI, EDIII-DVII, EDIII-DVIII, and EDIII-DVIV, as determined bycompetition ELISA.

FIG. 13A and FIG. 13B: demonstrate the binding profiles of 4E5A antibodyvariants for DV1 and DV2 (FIG. 13A) and for DV3 and DV4 (FIG. 13B), asdetermined by surface plasmon resonance.

FIG. 14: FIG. 14 demonstrates the single-chain variable fragment bindingof 4E5A antibody variants when expressed on the surface of yeast cells.

FIG. 15: FIG. 15 demonstrates the neutralization of DV4 reporter virusparticles by 4E5A antibody variants.

DEFINITIONS

In order for the present invention to be more readily understood,certain terms are first defined below; those of ordinary skill in theart will appreciate and understand the use and scope of these terms asdefined below and/or otherwise used herein.

Adult: As used herein, the term “adult” refers to a human eighteen yearsof age or older. Body weights among adults can vary widely with atypical range being 90 pounds to 250 pounds.

Affinity: As is known in the art, “affinity” is a measure of thetightness with a particular ligand (e.g., an antibody) binds to itspartner (e.g., an epitope). Affinities can be measured in differentways.

Amino acid: As used herein, term “amino acid,” in its broadest sense,refers to any compound and/or substance that can be incorporated into apolypeptide chain. In some embodiments, an amino acid has the generalstructure H₂N—C(H)(R)—COOH. In some embodiments, an amino acid is anaturally occurring amino acid. In some embodiments, an amino acid is asynthetic amino acid; in some embodiments, an amino acid is a d-aminoacid; in some embodiments, an amino acid is an 1-amino acid. “Standardamino acid” refers to any of the twenty standard 1-amino acids commonlyfound in naturally occurring peptides. “Nonstandard amino acid” refersto any amino acid, other than the standard amino acids, regardless ofwhether it is prepared synthetically or obtained from a natural source.As used herein, “synthetic amino acid” encompasses chemically modifiedamino acids, including but not limited to salts, amino acid derivatives(such as amides), and/or substitutions. Amino acids, including carboxy-and/or amino-terminal amino acids in peptides, can be modified bymethylation, amidation, acetylation, protecting groups, and/orsubstitution with other chemical groups that can change the peptide'scirculating half-life without adversely affecting their activity. Aminoacids may participate in a disulfide bond. Amino acids may comprise oneor posttranslational modifications, such as association with one or morechemical entities (e.g., methyl groups, acetate groups, acetyl groups,phosphate groups, formyl moieties, isoprenoid groups, sulfate groups,polyethylene glycol moieties, lipid moieties, carbohydrate moieties,biotin moieties, etc.). The term “amino acid” is used interchangeablywith “amino acid residue,” and may refer to a free amino acid and/or toan amino acid residue of a peptide. It will be apparent from the contextin which the term is used whether it refers to a free amino acid or aresidue of a peptide.

Animal: As used herein, the term “animal” refers to any member of theanimal kingdom. In some embodiments, “animal” refers to humans, ofeither sex and at any stage of development. In some embodiments,“animal” refers to non-human animals, at any stage of development. Incertain embodiments, the non-human animal is a mammal (e.g., a rodent, amouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, aprimate, and/or a pig). In some embodiments, animals include, but arenot limited to, mammals, birds, reptiles, amphibians, fish, insects,and/or worms. In certain embodiments, the animal is susceptible toinfection by DV. In some embodiments, an animal may be a transgenicanimal, genetically engineered animal, and/or a clone.

Antibody agent: As used herein, the term “antibody agent” refers to anagent that specifically binds to a particular antigen. In someembodiments, the term encompasses any polypeptide with immunoglobulinstructural elements sufficient to confer specific binding. Suitableantibody agents include, but are not limited to, human antibodies,primatized antibodies, chimeric antibodies, bi-specific antibodies,humanized antibodies, conjugated antibodies (i.e., antibodies conjugatedor fused to other proteins, radiolabels, cytotoxins), Small ModularImmunoPharmaceuticals (“SMIPs™”), single chain antibodies, cameloidantibodies, and antibody fragments. As used herein, the term “antibodyagent” also includes intact monoclonal antibodies, polyclonalantibodies, single domain antibodies (e.g., shark single domainantibodies (e.g., IgNAR or fragments thereof)), multispecific antibodies(e.g. bi-specific antibodies) formed from at least two intactantibodies, and antibody fragments so long as they exhibit the desiredbiological activity. In some embodiments, the term encompasses stapledpeptides. In some embodiments, the term encompasses one or moreantibody-like binding peptidomimetics. In some embodiments, the termencompasses one or more antibody-like binding scaffold proteins. In comeembodiments, the term encompasses monobodies or adnectins. In manyembodiments, an antibody agent is or comprises a polypeptide whose aminoacid sequence includes one or more structural elements recognized bythose skilled in the art as a complementarity determining region (CDR);in some embodiments an antibody agent is or comprises a polypeptidewhose amino acid sequence includes at least one CDR (e.g., at least oneheavy chain CDR and/or at least one light chain CDR) that issubstantially identical to one found in a reference antibody. In someembodiments an included CDR is substantially identical to a referenceCDR in that it is either identical in sequence or contains between 1-5amino acid substitutions as compared with the reference CDR. In someembodiments an included CDR is substantially identical to a referenceCDR in that it shows at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with thereference CDR. In some embodiments an included CDR is substantiallyidentical to a reference CDR in that it shows at least 96%, 96%, 97%,98%, 99%, or 100% sequence identity with the reference CDR. In someembodiments an included CDR is substantially identical to a referenceCDR in that at least one amino acid within the included CDR is deleted,added, or substituted as compared with the reference CDR but theincluded CDR has an amino acid sequence that is otherwise identical withthat of the reference CDR. In some embodiments an included CDR issubstantially identical to a reference CDR in that 1-5 amino acidswithin the included CDR are deleted, added, or substituted as comparedwith the reference CDR but the included CDR has an amino acid sequencethat is otherwise identical to the reference CDR. In some embodiments anincluded CDR is substantially identical to a reference CDR in that atleast one amino acid within the included CDR is substituted as comparedwith the reference CDR but the included CDR has an amino acid sequencethat is otherwise identical with that of the reference CDR. In someembodiments an included CDR is substantially identical to a referenceCDR in that 1-5 amino acids within the included CDR are deleted, added,or substituted as compared with the reference CDR but the included CDRhas an amino acid sequence that is otherwise identical to the referenceCDR. In some embodiments, an antibody agent is or comprises apolypeptide whose amino acid sequence includes structural elementsrecognized by those skilled in the art as an immunoglobulin variabledomain. In some embodiments, an antibody agent is a polypeptide proteinhaving a binding domain which is homologous or largely homologous to animmunoglobulin-binding domain

Antibody: As is known in the art, an “antibody” is an immunoglobulinthat binds specifically to a particular antigen. The term encompassesimmunoglobulins that are naturally produced in that they are generatedby an organism reacting to the antigen, and also those that aresynthetically produced or engineered. An antibody may be monoclonal orpolyclonal. An antibody may be a member of any immunoglobulin class,including any of the human classes: IgG, IgM, IgA, and IgD. A typicalimmunoglobulin (antibody) structural unit as understood in the art, isknown to comprise a tetramer. Each tetramer is composed of two identicalpairs of polypeptide chains, each pair having one “light” (approximately25 kD) and one “heavy” chain (approximately 50-70 kD). The N-terminus ofeach chain defines a variable region of about 100 to 110 or more aminoacids primarily responsible for antigen recognition. The terms “variablelight chain” (VL) and “variable heavy chain” (VH) refer to these lightand heavy chains respectively. Each variable region is furthersubdivided into hypervariable (HV) and framework (FR) regions. Thehypervariable regions comprise three areas of hypervariability sequencecalled complementarity determining regions (CDR 1, CDR 2 and CDR 3),separated by four framework regions (FR1, FR2, FR2, and FR4) which forma beta-sheet structure and serve as a scaffold to hold the HV regions inposition. The C-terminus of each heavy and light chain defines aconstant region consisting of one domain for the light chain (CL) andthree for the heavy chain (CH1, CH2 and CH3). In some embodiments, theterm “full length” is used in reference to an antibody to mean that itcontains two heavy chains and two light chains, optionally associated bydisulfide bonds as occurs with naturally-produced antibodies. In someembodiments, an antibody is produced by a cell. In some embodiments, anantibody is produced by chemical synthesis. In some embodiments, anantibody is derived from a mammal. In some embodiments, an antibody isderived from an animal such as, but not limited to, mouse, rat, horse,pig, or goat. In some embodiments, an antibody is produced using arecombinant cell culture system. In some embodiments, an antibody may bea purified antibody (for example, by immune-affinity chromatography). Insome embodiments, an antibody may be a human antibody. In someembodiments, an antibody may be a humanized antibody (antibody fromnon-human species whose protein sequences have been modified to increasetheir similarity to antibody variants produced naturally in humans). Insome embodiments, an antibody may be a chimeric antibody (antibody madeby combining genetic material from a non-human source, e.g., mouse, rat,horse, or pig, with genetic material from humans).

Antibody fragment: As used herein, an “antibody fragment” includes aportion of an intact antibody, such as, for example, the antigen-bindingor variable region of an antibody. Examples of antibody fragmentsinclude Fab, Fab′, F(ab′)2, and Fv fragments; triabodies; tetrabodies;linear antibodies; single-chain antibody molecules; and multi specificantibodies formed from antibody fragments. For example, antibodyfragments include isolated fragments, “Fv” fragments, consisting of thevariable regions of the heavy and light chains, recombinant single chainpolypeptide molecules in which light and heavy chain variable regionsare connected by a peptide linker (“ScFv proteins”), and minimalrecognition units consisting of the amino acid residues that mimic thehypervariable region. In many embodiments, an antibody fragment containssufficient sequence of the parent antibody of which it is a fragmentthat it binds to the same antigen as does the parent antibody; in someembodiments, a fragment binds to the antigen with a comparable affinityto that of the parent antibody and/or competes with the parent antibodyfor binding to the antigen. Examples of antigen binding fragments of anantibody include, but are not limited to, Fab fragment, Fab′ fragment,F(ab′)2 fragment, scFv fragment, Fv fragment, dsFv diabody, dAbfragment, Fd′ fragment, Fd fragment, and an isolated complementaritydetermining region (CDR) region. An antigen binding fragment of anantibody may be produced by any means. For example, an antigen bindingfragment of an antibody may be enzymatically or chemically produced byfragmentation of an intact antibody and/or it may be recombinantlyproduced from a gene encoding the partial antibody sequence.Alternatively or additionally, antigen binding fragment of an antibodymay be wholly or partially synthetically produced. An antigen bindingfragment of an antibody may optionally comprise a single chain antibodyfragment. Alternatively or additionally, an antigen binding fragment ofan antibody may comprise multiple chains which are linked together, forexample, by disulfide linkages. An antigen binding fragment of anantibody may optionally comprise a multimolecular complex. A functionalantibody fragment typically comprises at least about 50 amino acids andmore typically comprises at least about 200 amino acids.

Antiviral agent: As used herein, the term “antiviral agent” refers to aclass of medication used specifically for treating viral infections byinhibiting, deactivating, or destroying virus particles. In general, anantiviral agent may be or comprise a compound of any chemical class(e.g., a small molecule, metal, nucleic acid, polypeptide, lipid and/orcarbohydrate). In some embodiments, an antiviral agent is or comprisesan antibody or antibody mimic. In some embodiments, an antiviral agentis or comprises a nucleic acid agent (e.g., an antisenseoligonucleotide, a siRNA, a shRNA, etc) or mimic thereof. In someembodiments, an antiviral agent is or comprises a small molecule. Insome embodiments, an antiviral agent is or comprises anaturally-occurring compound (e.g., small molecule). In someembodiments, an antiviral agent has a chemical structure that isgenerated and/or modified by the hand of man.

Approximately: As used herein, the term “approximately” or “about,” asapplied to one or more values of interest, refers to a value that issimilar to a stated reference value. In certain embodiments, the term“approximately” or “about” refers to a range of values that fall within25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%,6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than orless than) of the stated reference value unless otherwise stated orotherwise evident from the context (except where such number wouldexceed 100% of a possible value).

Baby: As used herein, the term “baby” refers to a human under two yearsof age. Typical body weights for a baby rages from 3 pounds up to 20pounds.

Biologically active: As used herein, the phrase “biologically active”refers to a characteristic of any substance that has activity in abiological system (e.g., cell culture, organism, etc.). For instance, asubstance that, when administered to an organism, has a biologicaleffect on that organism, is considered to be biologically active. Inparticular embodiments, where a protein or polypeptide is biologicallyactive, a portion of that protein or polypeptide that shares at leastone biological activity of the protein or polypeptide is typicallyreferred to as a “biologically active” portion.

Characteristic portion: As used herein, the term “characteristicportion” is used, in the broadest sense, to refer to a portion of asubstance whose presence (or absence) correlates with presence (orabsence) of a particular feature, attribute, or activity of thesubstance. In some embodiments, a characteristic portion of a substanceis a portion that is found in the substance and in related substancesthat share the particular feature, attribute or activity, but not inthose that do not share the particular feature, attribute or activity.In certain embodiments, a characteristic portion shares at least onefunctional characteristic with the intact substance. For example, insome embodiments, a “characteristic portion” of a protein or polypeptideis one that contains a continuous stretch of amino acids, or acollection of continuous stretches of amino acids, that together arecharacteristic of a protein or polypeptide. In some embodiments, eachsuch continuous stretch generally contains at least 2, 5, 10, 15, 20,50, or more amino acids. In general, a characteristic portion of asubstance (e.g., of a protein, antibody, etc.) is one that, in additionto the sequence and/or structural identity specified above, shares atleast one functional characteristic with the relevant intact substance.In some embodiments, a characteristic portion may be biologicallyactive.

Child: As used herein, the term “child” refers to a human between twoand 18 years of age. Body weight can vary widely across ages andspecific children, with a typical range being 30 pounds to 150 pounds.

Combination therapy: The term “combination therapy”, as used herein,refers to those situations in which two or more different pharmaceuticalagents are administered in overlapping regimens so that the subject issimultaneously exposed to both agents.

Comparable: The term “comparable” is used herein to describe two (ormore) sets of conditions or circumstances that are sufficiently similarto one another to permit comparison of results obtained or phenomenaobserved. In some embodiments, comparable sets of conditions orcircumstances are characterized by a plurality of substantiallyidentical features and one or a small number of varied features. Thoseof ordinary skill in the art will appreciate that sets of conditions arecomparable to one another when characterized by a sufficient number andtype of substantially identical features to warrant a reasonableconclusion that differences in results obtained or phenomena observedunder the different sets of conditions or circumstances are caused by orindicative of the variation in those features that are varied.

Corresponding to: As used herein, the term “corresponding to” is oftenused to designate the position/identity of an amino acid residue in apolypeptide of interest. Those of ordinary skill will appreciate that,for purposes of simplicity, residues in a polypeptide are oftendesignated using a canonical numbering system based on a referencerelated polypeptide, so that an amino acid “corresponding to” a residueat position 190, for example, need not actually be the 190^(th) aminoacid in a particular amino acid chain but rather corresponds to theresidue found at 190 in the reference polypeptide; those of ordinaryskill in the art readily appreciate how to identify “corresponding”amino acids.

Dosage form: As used herein, the terms “dosage form” and “unit dosageform” refer to a physically discrete unit of a therapeutic protein(e.g., antibody) for the patient to be treated. Each unit contains apredetermined quantity of active material calculated to produce thedesired therapeutic effect. It will be understood, however, that thetotal dosage of the composition will be decided by the attendingphysician within the scope of sound medical judgment.

Dosing regimen: A “dosing regimen” (or “therapeutic regimen”), as thatterm is used herein, is a set of unit doses (typically more than one)that are administered individually to a subject, typically separated byperiods of time. In some embodiments, a given therapeutic agent has arecommended dosing regimen, which may involve one or more doses. In someembodiments, a dosing regimen comprises a plurality of doses each ofwhich are separated from one another by a time period of the samelength; in some embodiments, a dosing regimen comprises a plurality ofdoses and at least two different time periods separating individualdoses. In some embodiments, all doses within a dosing regimen are of thesame unit dose amount. In some embodiments, different doses within adosing regimen are of different amounts. In some embodiments, a dosingregimen comprises a first dose in a first dose amount, followed by oneor more additional doses in a second dose amount different from thefirst dose amount. In some embodiments, a dosing regimen comprises afirst dose in a first dose amount, followed by one or more additionaldoses in a second dose amount same as the first dose amount.

DVserotype: As used herein, the term “serotype” generally refers todistinct variations within DVs. The four different DV serotypes (DV1-4)comprising the DV genetic group differ from one another by approximately25% to 40% at the amino acid level. The four serotypes of DV vary inpathogenicities but all are prevalent in areas of Asia, Africa, Centraland South America. Infection with one of these serotypes provideslife-long immunity to that serotype however it also increases risk ofsevere disease upon a secondary infection from a heterologous DVserotype.

Epitope: As used herein, the term “epitope” has its meaning asunderstood in the art. It will be appreciated by those of ordinary skillin the art that an epitope also known as antigenic determinant, is amolecular region of an antigen that is recognized by the immune system,specifically by antibodies, B cells, or T cells. It will be furtherappreciated that epitopes can be composed of sugars, lipids, or aminoacids. The epitopes of protein antigens are divided into two categories,conformational epitopes and linear epitopes, based on their structureand interaction with the paratope (part of an antibody that recognizesthe epitope). A conformational epitope is composed of discontinuoussections of the antigen's amino acid sequence and these epitopesinteract with the paratope based on the 3-D surface features and shapeor tertiary structure of the antigen. Linear epitopes interact with theparatope based on their primary structure and a linear epitope is formedby a continuous sequence of amino acids from the antigen.

Expression: As used herein, “expression” of a nucleic acid sequencerefers to one or more of the following events: (1) production of an RNAtemplate from a DNA sequence (e.g., by transcription); (2) processing ofan RNA transcript (e.g., by splicing, editing, 5′ cap formation, and/or3′ end formation); (3) translation of an RNA into a polypeptide orprotein; and/or (4) post-translational modification of a polypeptide orprotein.

Functional: As used herein, a “functional” biological molecule is abiological molecule in a form in which it exhibits a property and/oractivity by which it is characterized.

Gene: As used herein, the term “gene” has its meaning as understood inthe art. It will be appreciated by those of ordinary skill in the artthat the term “gene” may include gene regulatory sequences (e.g.,promoters, enhancers, etc.) and/or intron sequences. It will further beappreciated that definitions of gene include references to nucleic acidsthat do not encode proteins but rather encode functional RNA moleculessuch as tRNAs, RNAi-inducing agents, etc. For the purpose of clarity wenote that, as used in the present application, the term “gene” generallyrefers to a portion of a nucleic acid that encodes a protein; the termmay optionally encompass regulatory sequences, as will be clear fromcontext to those of ordinary skill in the art. This definition is notintended to exclude application of the term “gene” to non-protein-codingexpression units but rather to clarify that, in most cases, the term asused in this document refers to a protein-coding nucleic acid.

Gene product or expression product: As used herein, the term “geneproduct” or “expression product” generally refers to an RNA transcribedfrom the gene (pre-and/or post-processing) or a polypeptide (pre- and/orpost-modification) encoded by an RNA transcribed from the gene.

Homology: As used herein, the term “homology” refers to the overallrelatedness between polymeric molecules, e.g., between nucleic acidmolecules (e.g., DNA molecules and/or RNA molecules) and/or betweenpolypeptide molecules. In some embodiments, polymeric molecules areconsidered to be “homologous” to one another if their sequences are atleast 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or 99% identical. In some embodiments, polymeric molecules areconsidered to be “homologous” to one another if their sequences are atleast 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or 99% similar.

Identity: As used herein, the term “identity” refers to the overallrelatedness between polymeric molecules, e.g., between nucleic acidmolecules (e.g., DNA molecules and/or RNA molecules) and/or betweenpolypeptide molecules. Calculation of the percent identity of twonucleic acid sequences, for example, can be performed by aligning thetwo sequences for optimal comparison purposes (e.g., gaps can beintroduced in one or both of a first and a second nucleic acid sequencesfor optimal alignment and non-identical sequences can be disregarded forcomparison purposes). In certain embodiments, the length of a sequencealigned for comparison purposes is at least 30%, at least 40%, at least50%, at least 60%, at least 70%, at least 80%, at least 90%, at least95%, or substantially 100% of the length of the reference sequence. Thenucleotides at corresponding nucleotide positions are then compared.When a position in the first sequence is occupied by the same nucleotideas the corresponding position in the second sequence, then the moleculesare identical at that position. The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences, taking into account the number of gaps, and the length ofeach gap, which needs to be introduced for optimal alignment of the twosequences. The comparison of sequences and determination of percentidentity between two sequences can be accomplished using a mathematicalalgorithm. For example, the percent identity between two nucleotidesequences can be determined using the algorithm of Meyers and Miller(CABIOS, 1989, 4: 11-17), which has been incorporated into the ALIGNprogram (version 2.0) using a PAM120 weight residue table, a gap lengthpenalty of 12 and a gap penalty of 4. The percent identity between twonucleotide sequences can, alternatively, be determined using the GAPprogram in the GCG software package using an NWSgapdna.CMP matrix.

Isolated: As used herein, the term “isolated” refers to a substanceand/or entity that has been (1) separated from at least some of thecomponents with which it was associated when initially produced (whetherin nature and/or in an experimental setting), and/or (2) produced,prepared, and/or manufactured by the hand of man. Isolated substancesand/or entities may be separated from about 10%, about 20%, about 30%,about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%,about 98%, about 99%, or more than about 99% of the other componentswith which they were initially associated. In some embodiments, isolatedagents are about 80%, about 85%, about 90%, about 91%, about 92%, about93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%,or more than about 99% pure. As used herein, a substance is “pure” if itis substantially free of other components. As used herein, calculationof percent purity of isolated substances and/or entities should notinclude excipients (e.g., buffer, solvent, water, etc.).

Mimotope: As used herein, the term “mimotope” refers to a macromoleculewhich mimics the structure of an epitope. In some embodiments, amimotope elicits an antibody response identical or similar to thatelicited by its corresponding epitope. In some embodiments, an antibodythat recognizes an epitope also recognizes a mimotope which mimics thatepitope. In some embodiments, a mimotope is a peptide. In someembodiments, a mimotope is a small molecule, carbohydrate, lipid, ornucleic acid. In some embodiments, mimotopes are peptide or non-peptidemimotopes of conserved DV epitopes. In some embodiments, by mimickingthe structure of a defined viral epitope, a mimotope interferes with theability of DV virus particles to bind to its natural binding partners(e.g., DV target receptor, Rab5, GRP78), e.g., by binding to the naturalbinding partner itself.

Mutant: As used herein, the term “mutant” refers to an entity that showssignificant structural identity with a reference entity but differsstructurally from the reference entity in the presence or level of oneor more chemical moieties as compared with the reference entity. In manyembodiments, a mutant also differs functionally from its referenceentity. In general, whether a particular entity is properly consideredto be a “mutant” of a reference entity is based on its degree ofstructural identity with the reference entity. As will be appreciated bythose skilled in the art, any biological or chemical reference entityhas certain characteristic structural elements. A mutant, by definition,is a distinct chemical entity that shares one or more suchcharacteristic structural elements. To give but a few examples, a smallmolecule may have a characteristic core structural element (e.g., amacrocycle core) and/or one or more characteristic pendent moieties sothat a mutant of the small molecule is one that shares the corestructural element and the characteristic pendent moieties but differsin other pendent moieties and/or in types of bonds present (single vsdouble, E vs Z, etc) within the core, a polypeptide may have acharacteristic sequence element comprised of a plurality of amino acidshaving designated positions relative to one another in linear orthree-dimensional space and/or contributing to a particular biologicalfunction, a nucleic acid may have a characteristic sequence elementcomprised of a plurality of nucleotide residues having designatedpositions relative to on another in linear or three-dimensional space.For example, a mutant polypeptide may differ from a referencepolypeptide as a result of one or more differences in amino acidsequence and/or one or more differences in chemical moieties (e.g.,carbohydrates, lipids, etc) covalently attached to the polypeptidebackbone. In some embodiments, a mutant polypeptide shows an overallsequence identity with a reference polypeptide that is at least 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 99%.Alternatively or additionally, in some embodiments, a mutant polypeptidedoes not share at least one characteristic sequence element with areference polypeptide. In some embodiments, the reference polypeptidehas one or more biological activities. In some embodiments, a mutantpolypeptide shares one or more of the biological activities of thereference polypeptide. In some embodiments, a mutant polypeptide lacksone or more of the biological activities of the reference polypeptide.In some embodiments, a mutant polypeptide shows a reduced level of oneor more biological activities as compared with the referencepolypeptide.

Nucleic acid: As used herein, the term “nucleic acid,” in its broadestsense, refers to any compound and/or substance that is or can beincorporated into an oligonucleotide chain. In some embodiments, anucleic acid is a compound and/or substance that is or can beincorporated into an oligonucleotide chain via a phosphodiester linkage.In some embodiments, “nucleic acid” refers to individual nucleic acidresidues (e.g., nucleotides and/or nucleosides). In some embodiments,“nucleic acid” refers to an oligonucleotide chain comprising individualnucleic acid residues. As used herein, the terms “oligonucleotide” and“polynucleotide” can be used interchangeably. In some embodiments,“nucleic acid” encompasses RNA as well as single and/or double-strandedDNA and/or cDNA. Furthermore, the terms “nucleic acid,” “DNA,” “RNA,”and/or similar terms include nucleic acid analogs, i.e., analogs havingother than a phosphodiester backbone. For example, the so-called“peptide nucleic acids,” which are known in the art and have peptidebonds instead of phosphodiester bonds in the backbone, are consideredwithin the scope of the present invention. The term “nucleotide sequenceencoding an amino acid sequence” includes all nucleotide sequences thatare degenerate versions of each other and/or encode the same amino acidsequence. Nucleotide sequences that encode proteins and/or RNA mayinclude introns. Nucleic acids can be purified from natural sources,produced using recombinant expression systems and optionally purified,chemically synthesized, etc. Where appropriate, e.g., in the case ofchemically synthesized molecules, nucleic acids can comprise nucleosideanalogs such as analogs having chemically modified bases or sugars,backbone modifications, etc. A nucleic acid sequence is presented in the5′ to 3′ direction unless otherwise indicated. The term “nucleic acidsegment” is used herein to refer to a nucleic acid sequence that is aportion of a longer nucleic acid sequence. In many embodiments, anucleic acid segment comprises at least 3, 4, 5, 6, 7, 8, 9, 10, or moreresidues. In some embodiments, a nucleic acid is or comprises naturalnucleosides (e.g., adenosine, thymidine, guanosine, cytidine, uridine,deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine);nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine,pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, C-5propynyl-cytidine, C-5 propynyl-uridine, 2-aminoadenosine,C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine,C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine,7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine,0(6)-methylguanine, and 2-thiocytidine); chemically modified bases;biologically modified bases (e.g., methylated bases); intercalatedbases; modified sugars (e.g., 2′-fluororibose, ribose, 2′-deoxyribose,arabinose, and hexose); and/or modified phosphate groups (e.g.,phosphorothioates and 5′-N-phosphoramidite linkages). In someembodiments, the present invention is specifically directed to“unmodified nucleic acids,” meaning nucleic acids (e.g., polynucleotidesand residues, including nucleotides and/or nucleosides) that have notbeen chemically modified in order to facilitate or achieve delivery.

Patient: As used herein, the term “patient” or “subject” refers to anyorganism to which a provided composition may be administered, e.g., forexperimental, diagnostic, prophylactic, cosmetic, and/or therapeuticpurposes. Typical patients include animals (e.g., mammals such as mice,rats, rabbits, non-human primates, and/or humans). In some embodiments,a patient is a human. A human includes pre and post natal forms.

Pharmaceutically acceptable: The term “pharmaceutically acceptable” asused herein, refers to substances that, within the scope of soundmedical judgment, are suitable for use in contact with the tissues ofhuman beings and animals without excessive toxicity, irritation,allergic response, or other problem or complication, commensurate with areasonable benefit/risk ratio.

Pharmaceutically acceptable carrier: As used herein, the term“pharmaceutically acceptable carrier” means apharmaceutically-acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, or solvent encapsulatingmaterial, involved in carrying or transporting the subject compound fromone organ, or portion of the body, to another organ, or portion of thebody. Each carrier must be “acceptable” in the sense of being compatiblewith the other ingredients of the formulation and not injurious to thepatient. Some examples of materials which can serve aspharmaceutically-acceptable carriers include: sugars, such as lactose,glucose and sucrose; starches, such as corn starch and potato starch;cellulose, and its derivatives, such as sodium carboxymethyl cellulose,ethyl cellulose and cellulose acetate; powdered tragacanth; malt;gelatin; talc; excipients, such as cocoa butter and suppository waxes;oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil,olive oil, corn oil and soybean oil; glycols, such as propylene glycol;polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol;esters, such as ethyl oleate and ethyl laurate; agar; buffering agents,such as magnesium hydroxide and aluminum hydroxide; alginic acid;pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol;pH buffered solutions; polyesters, polycarbonates and/or polyanhydrides;and other non-toxic compatible substances employed in pharmaceuticalformulations.

Pharmaceutical composition: As used herein, the term “pharmaceuticalcomposition” refers to an active agent, formulated together with one ormore pharmaceutically acceptable carriers. In some embodiments, activeagent is present in unit dose amount appropriate for administration in atherapeutic regimen that shows a statistically significant probabilityof achieving a predetermined therapeutic effect when administered to arelevant population. In some embodiments, pharmaceutical compositionsmay be specially formulated for administration in solid or liquid form,including those adapted for the following: oral administration, forexample, drenches (aqueous or non-aqueous solutions or suspensions),tablets, e.g., those targeted for buccal, sublingual, and systemicabsorption, boluses, powders, granules, pastes for application to thetongue; parenteral administration, for example, by subcutaneous,intramuscular, intravenous or epidural injection as, for example, asterile solution or suspension, or sustained-release formulation;topical application, for example, as a cream, ointment, or acontrolled-release patch or spray applied to the skin, lungs, or oralcavity; intravaginally or intrarectally, for example, as a pessary,cream, or foam; sublingually; ocularly; transdermally; or nasally,pulmonary, and to other mucosal surfaces.

Polypeptide: As used herein, a “polypeptide”, generally speaking, is astring of at least two amino acids attached to one another by a peptidebond. In some embodiments, a polypeptide may include at least 3-5 aminoacids, each of which is attached to others by way of at least onepeptide bond. Those of ordinary skill in the art will appreciate thatpolypeptides sometimes include “non-natural” amino acids or otherentities that nonetheless are capable of integrating into a polypeptidechain, optionally.

Protein: As used herein, the term “protein” refers to a polypeptide(i.e., a string of at least two amino acids linked to one another bypeptide bonds). Proteins may include moieties other than amino acids(e.g., may be glycoproteins, proteoglycans, etc.) and/or may beotherwise processed or modified. Those of ordinary skill in the art willappreciate that a “protein” can be a complete polypeptide chain asproduced by a cell (with or without a signal sequence), or can be acharacteristic portion thereof. Those of ordinary skill will appreciatethat a protein can sometimes include more than one polypeptide chain,for example linked by one or more disulfide bonds or associated by othermeans. Polypeptides may contain 1-amino acids, d-amino acids, or bothand may contain any of a variety of amino acid modifications or analogsknown in the art. Useful modifications include, e.g., terminalacetylation, amidation, methylation, etc. In some embodiments, proteinsmay comprise natural amino acids, non-natural amino acids, syntheticamino acids, and combinations thereof. The term “peptide” is generallyused to refer to a polypeptide having a length of less than about 100amino acids, less than about 50 amino acids, less than 20 amino acids,or less than 10 amino acids. In some embodiments, proteins areantibodies, antibody fragments, biologically active portions thereof,and/or characteristic portions thereof.

Recurrent DV infection: As used herein, a “recurrent DV infection”refers to reemergence of clinical and/or laboratory evidence ofinfection, e.g., one or more symptoms of infection or the presence ofcirculating DV particles and/or DV particles in the subject's liver.

Refractory: The term “refractory” as used herein, refers to any subjectthat does not respond with an expected clinical efficacy following theadministration of provided compositions as normally observed bypracticing medical personnel.

Serotype: In general, a “serotype” or “serovar” refers to distinctvariations within a species of bacteria or viruses or among immune cellsof different individuals. These microorganisms are typically classifiedtogether based on their cell surface antigens, allowing theepidemiologic classification of organisms to the sub-species level.

Small Molecule: In general, a “small molecule” is a molecule that isless than about 5 kilodaltons (kD) in size. In some embodiments, thesmall molecule is less than about 4 kD, 3 kD, about 2 kD, or about 1 kD.In some embodiments, the small molecule is less than about 800 daltons(D), about 600 D, about 500 D, about 400 D, about 300 D, about 200 D, orabout 100 D. In some embodiments, a small molecule is less than about2000 g/mol, less than about 1500 g/mol, less than about 1000 g/mol, lessthan about 800 g/mol, or less than about 500 g/mol. In some embodiments,small molecules are non-polymeric. In some embodiments, in accordancewith the present invention, small molecules are not proteins,polypeptides, oligopeptides, peptides, polynucleotides,oligonucleotides, polysaccharides, glycoproteins, proteoglycans, etc.

Substantially: As used herein, the term “substantially” refers to thequalitative condition of exhibiting total or near-total extent or degreeof a characteristic or property of interest. One of ordinary skill inthe biological arts will understand that biological and chemicalphenomena rarely, if ever, go to completion and/or proceed tocompleteness or achieve or avoid an absolute result. The term“substantially” is therefore used herein to capture the potential lackof completeness inherent in many biological and chemical phenomena.

Substantial sequence homology: The phrase “substantial homology” is usedherein to refer to a comparison between amino acid or nucleic acidsequences. As will be appreciated by those of ordinary skill in the art,two sequences are generally considered to be “substantially homologous”if they contain homologous residues in corresponding positions.Homologous residues may be identical residues. Alternatively, homologousresidues may be non-identical residues will appropriately similarstructural and/or functional characteristics. For example, as is wellknown by those of ordinary skill in the art, certain amino acids aretypically classified as “hydrophobic” or “hydrophilic” amino acids,and/or as having “polar” or “non-polar” side chains Substitution of oneamino acid for another of the same type may often be considered a“homologous” substitution. Removal (e.g., deletion) of a single aminoacid may often be considered a “null” substitution of that amino acid.Typical amino acid categorizations are summarized below:

Alanine Ala A nonpolar neutral 1.8 Arginine Arg R polar positive −4.5Asparagine Asn N polar neutral −3.5 Aspartic acid Asp D polar negative−3.5 Cysteine Cys C nonpolar neutral 2.5 Glutamic acid Glu E polarnegative −3.5 Glutamine Gln Q polar neutral −3.5 Glycine Gly G nonpolarneutral −0.4 Histidine His H polar positive −3.2 Isoleucine Ile Inonpolar neutral 4.5 Leucine Leu L nonpolar neutral 3.8 Lysine Lys Kpolar positive −3.9 Methionine Met M nonpolar neutral 1.9 PhenylalaninePhe F nonpolar neutral 2.8 Proline Pro P nonpolar neutral −1.6 SerineSer S polar neutral −0.8 Threonine Thr T polar neutral −0.7 TryptophanTrp W nonpolar neutral −0.9 Tyrosine Tyr Y polar neutral −1.3 Valine ValV nonpolar neutral 4.2 Ambiguous Amino Acids 3-Letter 1-LetterAsparagine or aspartic acid Asx B Glutamine or glutamic acid Glx ZLeucine or Isoleucine Xle J Unspecified or unknown amino acid Xaa X

As is well known in this art, amino acid or nucleic acid sequences maybe compared using any of a variety of algorithms, including thoseavailable in commercial computer programs such as BLASTN for nucleotidesequences and BLASTP, gapped BLAST, and PSI-BLAST for amino acidsequences. Exemplary such programs are described in Altschul, et al.,Basic local alignment search tool, J. Mol. Biol., 215(3): 403-410, 1990;Altschul, et al., Methods in Enzymology; Altschul, et al., “Gapped BLASTand PSI-BLAST: a new generation of protein database search programs”,Nucleic Acids Res. 25:3389-3402, 1997; Baxevanis, et al.,Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins,Wiley, 1998; and Misener, et al., (eds.), Bioinformatics Methods andProtocols (Methods in Molecular Biology, Vol. 132), Humana Press, 1999;all of the foregoing of which are incorporated herein by reference. Inaddition to identifying homologous sequences, the programs mentionedabove typically provide an indication of the degree of homology. In someembodiments, two sequences are considered to be substantially homologousif at least 50%, at least 55%, at least 60%, at least 65%, at least 70%,at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99% or more of their correspondingresidues are homologous over a relevant stretch of residues. In someembodiments, the relevant stretch is a complete sequence. In someembodiments, the relevant stretch is at least 10, at least 15, at least20, at least 25, at least 30, at least 35, at least 40, at least 45, atleast 50, at least 55, at least 60, at least 65, at least 70, at least75, at least 80, at least 85, at least 90, at least 95, at least 100, atleast 125, at least 150, at least 175, at least 200, at least 225, atleast 250, at least 275, at least 300, at least 325, at least 350, atleast 375, at least 400, at least 425, at least 450, at least 475, atleast 500 or more residues.

Substantial identity: The phrase “substantial identity” is used hereinto refer to a comparison between amino acid or nucleic acid sequences.As will be appreciated by those of ordinary skill in the art, twosequences are generally considered to be “substantially identical” ifthey contain identical residues in corresponding positions. As is wellknown in this art, amino acid or nucleic acid sequences may be comparedusing any of a variety of algorithms, including those available incommercial computer programs such as BLASTN for nucleotide sequences andBLASTP, gapped BLAST, and PSI-BLAST for amino acid sequences. Exemplarysuch programs are described in Altschul, et al., Basic local alignmentsearch tool, J. Mol. Biol., 215(3): 403-410, 1990; Altschul, et al.,Methods in Enzymology; Altschul et al., Nucleic Acids Res. 25:3389-3402,1997; Baxevanis et al., Bioinformatics: A Practical Guide to theAnalysis of Genes and Proteins, Wiley, 1998; and Misener, et al.,(eds.), Bioinformatics Methods and Protocols (Methods in MolecularBiology, Vol. 132), Humana Press, 1999. In addition to identifyingidentical sequences, the programs mentioned above typically provide anindication of the degree of identity. In some embodiments, two sequencesare considered to be substantially identical if at least 50%, 55%, 60%,65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or more of their corresponding residues are identical over arelevant stretch of residues. In some embodiments, the relevant stretchis a complete sequence. In some embodiments, the relevant stretch is atleast 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85,90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400,425, 450, 475, 500 or more residues.

Suffering from: An individual who is “suffering from” a disease,disorder, or condition (e.g., DV) has been diagnosed with and/orexhibits one or more symptoms of the disease, disorder, or condition. DVinfection is frequently asymptomatic. In some embodiments, an individualwho is suffering from DV has been exposed to and/or infected with DV,but does not display any symptoms of DV infection and/or has not beendiagnosed with DV infection. In some embodiments, an individual who issuffering from DV is an individual who has one or more DV particles inhis/her blood.

Susceptible to: An individual who is “susceptible to” a disease,disorder, or condition (e.g., DV) is at risk for developing the disease,disorder, or condition. In some embodiments, an individual who issusceptible to a disease, disorder, or condition does not display anysymptoms of the disease, disorder, or condition. In some embodiments, anindividual who is susceptible to a disease, disorder, or condition hasnot been diagnosed with the disease, disorder, and/or condition. In someembodiments, an individual who is susceptible to a disease, disorder, orcondition is an individual who has been exposed to conditions associatedwith development of the disease, disorder, or condition (e.g., theindividual has been exposed to DV). In some embodiments, a risk ofdeveloping a disease, disorder, and/or condition is a population-basedrisk (e.g., intravenous drug users; recipients of donated blood, bloodproducts, and organs prior to 1992, when such products began to bescreened; healthcare workers handling needles; babies born toDV-infected mothers; etc.).

Symptoms are reduced: According to the present invention, “symptoms arereduced” when one or more symptoms of a particular disease, disorder orcondition is reduced in magnitude (e.g., intensity, severity, etc.) orfrequency. For purposes of clarity, a delay in the onset of a particularsymptom is considered one form of reducing the frequency of thatsymptom. To give but a few examples, exemplary symptoms of DV include,but are not limited to, sudden onset of fever, high fever (often over40° C.), muscle and joint pains, headache, vomiting, diarrhea,occurrence of a rash as flushed skin or measles-like rash, petechiae(small red spots caused by broken capillaries that do not disappear whenskin is pressed), bleeding from the mucous membranes, low white bloodcell count, low platelets, metabolic acidosis, elevated level ofaminotransferase from the liver, plasma leakage resulting inhemoconcentration (indicated by a rising hematocrit) andhypoalbuminemia, fluid accumulation in the chest and abdominal cavity(e.g., pleural effusion or ascites), gastrointestinal bleeding, shockand hemorrhage, positive tourniquet test, hypotension, infection of thebrain or heart, impairment of vital organs (e.g., liver), neurologicaldisorders such as transverse myelitis, and/or combinations thereof. Itis not intended that the present invention be limited only to caseswhere the symptoms are eliminated. The present invention specificallycontemplates treatment such that one or more symptoms is/are reduced(and the condition of the subject is thereby “improved”), albeit notcompletely eliminated.

Therapeutic agent: As used herein, the phrase “therapeutic agent” refersto any agent that elicits a desired pharmacological effect whenadministered to an organism. In some embodiments, an agent is consideredto be a therapeutic agent if it demonstrates a statistically significanteffect across an appropriate population. In some embodiments, theappropriate population may be a population of model organisms. In someembodiments, an appropriate population may be defined by variouscriteria, such as a certain age group, gender, genetic background,preexisting clinical conditions, etc. In some embodiments, a therapeuticagent is any substance that can be used to alleviate, ameliorate,relieve, inhibit, prevent, delay onset of, reduce severity of, and/orreduce incidence of one or more symptoms or features of a disease,disorder, and/or condition.

Therapeutically effective amount: As used herein, the term“therapeutically effective amount” refers to an amount of a therapeuticprotein which confers a therapeutic effect on the treated subject, at areasonable benefit/risk ratio applicable to any medical treatment. Thetherapeutic effect may be objective (i.e., measurable by some test ormarker) or subjective (i.e., subject gives an indication of or feels aneffect). In particular, the “therapeutically effective amount” refers toan amount of a therapeutic protein or composition effective to treat,ameliorate, or prevent a desired disease or condition, or to exhibit adetectable therapeutic or preventative effect, such as by amelioratingsymptoms associated with the disease, preventing or delaying the onsetof the disease, and/or also lessening the severity or frequency ofsymptoms of the disease. A therapeutically effective amount is commonlyadministered in a dosing regimen that may comprise multiple unit doses.For any particular therapeutic protein, a therapeutically effectiveamount (and/or an appropriate unit dose within an effective dosingregimen) may vary, for example, depending on route of administration, oncombination with other pharmaceutical agents. Also, the specifictherapeutically effective amount (and/or unit dose) for any particularpatient may depend upon a variety of factors including the disorderbeing treated and the severity of the disorder; the activity of thespecific pharmaceutical agent employed; the specific compositionemployed; the age, body weight, general health, sex and diet of thepatient; the time of administration, route of administration, and/orrate of excretion or metabolism of the specific fusion protein employed;the duration of the treatment; and like factors as is well known in themedical arts.

Treatment: As used herein, the term “treatment” (also “treat” or“treating”) refers to any administration of a substance (e.g., providedcompositions) that partially or completely alleviates, ameliorates,relives, inhibits, delays onset of, reduces severity of, and/or reducesincidence of one or more symptoms, features, and/or causes of aparticular disease, disorder, and/or condition (e.g., DV). Suchtreatment may be of a subject who does not exhibit signs of the relevantdisease, disorder and/or condition and/or of a subject who exhibits onlyearly signs of the disease, disorder, and/or condition. Alternatively oradditionally, such treatment may be of a subject who exhibits one ormore established signs of the relevant disease, disorder and/orcondition. In some embodiments, treatment may be of a subject who hasbeen diagnosed as suffering from the relevant disease, disorder, and/orcondition. In some embodiments, treatment may be of a subject known tohave one or more susceptibility factors that are statisticallycorrelated with increased risk of development of the relevant disease,disorder, and/or condition.

Unit dose: The expression “unit dose” as used herein refers to an amountadministered as a single dose and/or in a physically discrete unit of apharmaceutical composition. In many embodiments, a unit dose contains apredetermined quantity of an active agent. In some embodiments, a unitdose contains an entire single dose of the agent. In some embodiments,more than one unit dose is administered to achieve a total single dose.In some embodiments, administration of multiple unit doses is required,or expected to be required, in order to achieve an intended effect. Aunit dose may be, for example, a volume of liquid (e.g., an acceptablecarrier) containing a predetermined quantity of one or more therapeuticagents, a predetermined amount of one or more therapeutic agents insolid form, a sustained release formulation or drug delivery devicecontaining a predetermined amount of one or more therapeutic agents,etc. It will be appreciated that a unit dose may be present in aformulation that includes any of a variety of components in addition tothe therapeutic agent(s). For example, acceptable carriers (e.g.,pharmaceutically acceptable carriers), diluents, stabilizers, buffers,preservatives, etc., may be included as described infra. It will beappreciated by those skilled in the art, in many embodiments, a totalappropriate daily dosage of a particular therapeutic agent may comprisea portion, or a plurality, of unit doses, and may be decided, forexample, by the attending physician within the scope of sound medicaljudgment. In some embodiments, the specific effective dose level for anyparticular subject or organism may depend upon a variety of factorsincluding the disorder being treated and the severity of the disorder;activity of specific active compound employed; specific compositionemployed; age, body weight, general health, sex and diet of the subject;time of administration, and rate of excretion of the specific activecompound employed; duration of the treatment; drugs and/or additionaltherapies used in combination or coincidental with specific compound(s)employed, and like factors well known in the medical arts.

Vaccination: As used herein, the term “vaccination” refers to theadministration of a composition intended to generate an immune response,for example to a disease-causing agent. For the purposes of the presentinvention, vaccination can be administered before, during, and/or afterexposure to a disease-causing agent, and in certain embodiments, before,during, and/or shortly after exposure to the agent. In some embodiments,vaccination includes multiple administrations, appropriately spaced intime, of a vaccinating composition.

Vector: As used herein, “vector” refers to a nucleic acid moleculecapable of transporting another nucleic acid to which it is associated.In some embodiment, vectors are capable of extra-chromosomal replicationand/or expression of nucleic acids to which they are linked in a hostcell such as a eukaryotic and/or prokaryotic cell. Vectors capable ofdirecting the expression of operatively linked genes are referred toherein as “expression vectors.”

Wild-type: As used herein, the term “wild-type” has its art-understoodmeaning that refers to an entity having a structure and/or activity asfound in nature in a “normal” (as contrasted with mutant, diseased,altered, etc) state or context. Those of ordinary skill in the art willappreciate that wild type genes and polypeptides often exist in multipledifferent forms (e.g., alleles).

DV Nomenclature

It is well known by those skilled in the art that DV nomenclaturetypically utilizes Roman numerals (e.g., “I,” “II,” “III,” “IV,” etc.)or Arabic numerals (e.g., “1”, “2”, “3”, “4”, etc.) that represents DVgenotype and a lowercase letter (e.g., “a,” “b,” etc.) that representsDV subtype. Although the rules of nomenclature are generally accepted inthe art, those of ordinary skill in the art recognize that the rules ofnomenclature are not always strictly followed in publications,presentations, conversation, etc. Thus, those skilled in the art wouldrecognize that, for example, it is implicit that “DV Ia”, “DV genotypeIa”, “DV subtype Ia”, “DV1a,” “DV genotype 1a,” and “DV subtype 1a”could be used interchangeably by one of skill in the art, and that allsix terms are intended to refer to DV genotype I, subtype a.

As used herein, Roman numerals (e.g., “I,” “II,” “III,” “IV,” etc.) orArabic numerals (e.g., “1”, “2”, “3”, “4”, etc.) are used to refer to DVgenotype, and lowercase letters (e.g., “a,” “b,” etc.) are used to referto DV subtypes. It will also be understood that, when DV of a particulargenotype is referred to herein, it is meant to encompass all subtypes ofthe named genotype. To give but one example, “genotype I” is used hereinto refer to all subtypes of genotype I (e.g., genotype I, subtype a;genotype I, subtype b; etc.).

As used herein, any Roman numeral (e.g., “I,” “II,” “III,” “IV,” etc.)that is present after the genotype and subtype designations will beunderstood to refer to the DV strain. Additionally, any Arabic numeral(e.g., “1”, “2”, “3”, “4”, etc.) that is present after the genotype andsubtype designations will be understood to refer to the DV strain.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS

The present invention provides useful anti-DV antibody agents withparticular structural and/or functional characteristics, as well ascompositions and methods relating to such antibody agents.

Dengue Virus (DV) infection

DV infection represents a major arthropod-borne viral disease, with over3.5 billion people living in areas of risk for the disease, and over 200million infections worldwide, resulting in 21,000 deaths per year.Notably, the annual average number of reported Dengue Virus infections,the geographical spread, and the severity of disease have all increaseddramatically in recent years. Dengue Virus epidemics can causesignificant morbidity, leading to substantial economic costs and healthcare impacts (Guzman et al, 2010 Nature Reviews Microbiol. 8:S7-16).

DV infection is caused by any of the four related viruses primarilytransmitted by Aedes aegypti mosquitoes and is endemic to tropical andsub-tropical regions. Infection in a mammal is initiated by injection ofthe DV during the blood meal of an infected Aedes mosquito, whereby theDV is primarily deposited in the extravascular tissues. The incubationperiod of DV after a mosquito bite is between 3 to 14 days. Dendriticcells, monocytes, and macrophages are among the first targets of DV.After initial replication in the skin and lymphatic ganglia, DV appearsin the blood in the course of the acute febrile stage, generally 3 to 5days.

Routine laboratory diagnosis of Dengue Virus infection is based onisolation of the DV and/or detection of antibodies specific to DV.Infection can cause several different syndromes, influenced by ageand/or immunological status of the infected individual. Primary DVinfection may be asymptomatic or may result in Dengue Fever. DengueFever is characterized by a high fever that typically has two phases andat least one additional symptom such as headache (often severe), pain(which can be severe) in any of a variety of body parts (e.g., eye,joint, muscle, bone, abdomen), skin eruptions or rash, mild bleedingmanifestation (e.g., nose or gum bleeding, petechiae, easy bruising),lymphadenopathy, vomiting, discolored (black) stools, mood effects suchas prostration, drowsiness or irritability, skin that is pale, cold, orclammy, difficulty breathing, low white cell count, circulating viralparticles in one or more of an organism's tissues (e.g., blood, bonemarrow, etc) and/or organs (e.g., liver) (see, for example, Center forDisease Control description; see also US 2011/0189226). Reducedleukocyte and platelet numbers frequently occur.

Dengue Hemorrhagic Fever (DHF) is a potentially deadly complication ofDV infection. DHF is characterized by extreme lethargy and drowsiness,coupled with the high fever and other symptoms associated with DengueFever. Increased vascular permeability and abnormal homeostasis can leadto a decrease in blood volume, hypotension, and in severe cases,hypovolemic shock and internal bleeding. Two factors that appear to playa major role in the occurrence of hemorrhagic Dengue Fever are: rapidviral replication with a high level of viremia; and a major inflammatoryresponse with the release of high levels of inflammatory mediators.Without treatment, the mortality rate for hemorrhagic Dengue Fever canreach 10%.

Children are particularly susceptible to the effects of DV infection,which can increase dramatically with repeated exposure. During initialDengue Virus infections, most children experience subclinical infectionor mild undifferentiated febrile syndromes. During secondary DengueVirus infections the pathophysiology of the disease often changesdramatically. Sequential infections can result in an acute vascularpermeability syndrome known as Dengue Shock Syndrome (DSS). DSS isusually a progression of DHF and is frequently fatal. DSS ischaracterized by rapid and poor volume pulse, hypotension, coldextremities, and restlessness. Without medical intervention, thefatality rate for DSS can reach 40-50% (Thullier et al, 1999 Journal ofBiotechnology 69:183-190). The severity of DSS is age-dependent, withvascular leakage being most severe in young children.

DV infections in adults are often accompanied by a tendency for bleedingthat can lead to severe hemorrhage. DV infections can belife-threatening when they occur in individuals with asthma, diabetes,and/or other chronic diseases (Guzman et al, 2010 Nature ReviewsMicrobiol. 8:S7-16).

The leading theory proposed to explain the increased risk of severedisease in secondary cases of DV is antibody dependent enhancement(ADE). Dengue Viruses (DVs) display antibody epitopes that are unique toeach serotype as well as epitopes that are shared between or amongserotypes. A subject has experienced (and recovered from) a primary DVinfection may develops robust antibody responses that cross react withall DV serotypes (DV1-4). However, despite the cross reactivity,antibodies only prevent re-infection by the same (homologous) serotypeand individuals are susceptible to subsequent infections with different(heterologous) serotypes. Individuals experiencing a secondary Dengueinfection with a new serotype face a much greater risk of developingDHF, indicating that pre-existing immunity to DV can exacerbate disease.The ADE theory of DV postulates that weakly neutralizing antibodies fromthe first infection bind to the second serotype and enhance infection ofFcγR bearing myeloid cells such as monocytes and macrophages (Wahala etal., 2011 Viruses 3: 2374-2395).

At least three types of mechanisms have been proposed to explaindevelopment of severe forms of DV infection: (i) they may be caused byparticularly virulent virus strains; (ii) pre-existing subneutralizingantibodies could enhance the antibody-mediated uptake of DV by monocytesor macrophages, which are designated as host cells of DV (e.g., ADE);and (iii) antibodies directed against a non-structural protein of thevirus (NS1) may cross-react with fibrinogen, thrombocytes andendothelial cells, thus triggering hemorrhages.

Currently, there is no specific treatment for Dengue Fever. Recommendedtherapies address symptoms, and include bed rest, control of the feverand pain through antipyretics and/or analgesics, and adequate hydration.Efforts focus on balancing liquid losses, replacement of coagulationfactors and the infusion of heparin. The sequence and antigenicvariability of DVs have challenged efforts to develop effective vaccinesor therapeutics (Whitehead et al., 2007 Nature Reviews Microbiology5:518-528). Unfortunately, the leading vaccine candidate recentlydemonstrated protective efficacy of only 30% in a phase II study (Thomaset al., 2011 Curr Op Infectious Disease 24:442-450; Sabchareon et al.,2012 Lancet 380(9853): 1559-1567). Therefore, there is a need for thedevelopment of improved DV therapies, vaccines. Particularly valuablewould be the development of treatments applicable to all DV serotypes.Such a therapy would have a tremendous impact on human health,especially in developing countries.

DV Antigens

DV infections are caused by four viruses (DV1-4), which are of similarserological type but differ antigenically. DVs are positivesingle-stranded RNA viruses belonging to the genus flavivirus within theFlaviviridae family. The virion comprises a spherical particle, 40-50 nmin diameter, with a lipopolysaccharide envelope. The RNA genome, whichis approximately 11 kb in length, comprises a 5′ type I end but lacks a3′ poly-A tail. The organization of the genome comprises the followingelements: a 5′ non-coding region (NCR), a region encoding structuralproteins (capsid (C), pre-membrane/membrane (prM/M), envelope (E)) and aregion encoding non-structural proteins(NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5) and a 3′ NCR.

The viral genomic RNA is associated with the capsid proteins to form anucleocapsid. As typical of flaviviruses, the Dengue viral genomeencodes an uninterrupted coding region which is translated into a singlepolyprotein which is post-translationally processed. Importantbiological properties of DV, include receptor binding, hemagglutinationof erythrocytes, induction of neutralizing antibodies and the protectiveimmune response, are associated with the E protein (Wahala et al., 2011Viruses 3:2374-2395).

The PrM protein, a glycoprotein of about 19 kDa, contains six highlyconserved cysteine residues forming three disulfide bridges and iscleaved to Pr and M proteins by furin or furin-like protease duringmaturation.

The NS1 protein, also a glycoprotein of about 40 kDa, contains 12 highlyconserved cysteine residues forming six disulfide bridges and is presentintracellularly, on the cell surface, and outside the cells (Lai et al.,2008 Journal of Virology 82(13):6631-43).

The E protein, a glycoprotein of approximately 55 kDa, contains 12strictly conserved cysteine residues forming six disulfide bridges andis present as a heterodimer with PrM protein before the maturation ofthe virion. X-ray crystallographic studies of the ectodomain of Eprotein have revealed three distinct beta-barrel domains connected tothe viral membrane by a helical stem anchor and two antiparalleltransmembrane domains. Domain III (EDIII) adopts an immunoglobulin-likefold and has been suggested to play a critical role in receptorinteractions. Domain II (EDII) is an elongated domain composed of twolong finger-like structures and contains a highly conserved 13 aminoacid fusion loop (EDII-FL) at the tip, and participates in the membranefusion and dimerization of E protein. The central domain of E (domain I;EDI) is a nine-stranded β-barrel that is connected to EDIII and EDII byone and four flexible linkers, respectively. E proteins are importantfor viral assembly, receptor attachment, entry, viral fusion, andpossibly immune evasion during the flavivirus life cycle and, thus, aredynamic proteins required to adopt several distinct conformations andarrangements on the virus particle. Moreover, E protein is the majortarget of both neutralizing and enhancing antibodies (Lai et al., 2008Journal of Virology 82:6631-6643; Pierson et al., 2008 Cell Host &Microbe 4:229-38).

DVs are assembled on the membrane of the endoplasmic reticulum (ER) andthe virus buds into the lumen of the ER as immature virus particles.Unlike mature virus particles that have a smooth surface, immature virusparticles that bud into the ER have a rough surface created by trimersof E/prM heterodimers that form sixty spiked projections withicosahedral symmetry on the viral envelope (Perera et al., 2008 Antivir.Res. 80 11-22). The E proteins of each trimer project away from thesurface of the virion and interact with prM via the distal end of EDIIincluding the fusion loop. PrM on immature virions restricts the abilityof E proteins to undergo oligomeric rearrangement in the low pHGolgi-derived secretory compartments during viral egress, thuspreventing premature and adventitious fusion (Guirakhoo et al., 1991Journal of Virology 72:1323-1329; Heinz et al., 1994 Journal of Virology198(1):109-117). As immature virions traffic through the acidiccompartments of the trans-Golgi network (TGN), changes in theorientation of prM and E proteins unmask a site for the cellular serineprotease furin. In this low pH environment, the E proteins of immaturevirions form antiparallel dimers that lie flat against the surface ofthe virion and are arranged with T=3 quasi-icosahedral symmetry (Yu etal., 2009 Journal of Virology 83(23):12101-12107). The prM proteincontinues to mask the fusion loop of EDII until it is released afterfurin cleavage and a transition to neutral pH occurs in theextracellular space. The resulting mature and infectious viruses arerelatively smooth particles composed of 90 E protein dimers and 180copies of the ˜70 amino acid M protein. In this configuration, Eproteins on the mature DV exist in three distinct environments definedby their proximity to the 2-, 3-, or 5-fold axis of symmetry (Kuhn etal., 2002 Cell 108:717-25). Thus, all the E protein subunits are not inidentical environments on the viral surface and steric and otherconsiderations result in preferential interactions of some E subunitsover others with receptors and antibodies.

Antibodies recognizing the highly conserved fusion loop on E proteindemonstrate broad reactivity to all four DV serotypes; however theirneutralization potency is typically limited, presumably due to thisepitope being largely inaccessible in mature DV. Some antibodies whichrecognize the ‘A’ β-strand of E protein domain III (EDIII) have beenshown to potently neutralize particular DV strains, but are not known tobe effective against all four serotypes (Lok et al., Nature Structural &Molecular Biol. 15:312-317). The ‘A’ β-strand is part of a sub complexepitope centered at positions 305-308 (DV3 numbering) on the EDIII.

As described herein, the present invention encompasses the finding thatthe E antigen, and particularly the EDIII domain can serve as a usefulantigenic target for broad-spectrum anti-DV antibody agents. Theinvention particularly demonstrates that antibodies that bind to the Eantigen (e.g., to the EDIII domain) but do not neutralize all DVserotypes can be rationally engineered to produce variants, and/or otherantibody agents, that do neutralize all of DV serotypes 1-4 (see, e.g.,FIG. 3). Furthermore, the present invention demonstrates that antibodiesthat bind to the E antigen (e.g., to the EDIII domain) and neutralizesome but not all DV serotypes can be rationally engineered to producevariants, and/or other antibody agents, that have gained neutralizationactivity, as compared with the parent antibody, against one or moreparticular strains and/or serotypes, without significantly depletingtheir activity, as compared with the parent antibody, against certainother strains and/or subtypes.

4E11 Antibody

Antibodies have proven to be an effective class of antiviraltherapeutics, in part due to their high biochemical specificity andtheir established safety record. Additionally, antibodies have a longserum half-life (˜21 days), enabling prophylactic uses in people, anapplication of particular need for infectious diseases which show rapidoutbreaks, including Dengue Virus.

Antibodies that protect against flavivirus infection are believed to actthrough multiple mechanisms, including one or more of (1) directneutralization of receptor binding, (2) inhibition of viral fusion, (3)Fc-γ-receptor-dependent viral clearance, (4) complement-mediated lysisof virus or infected cells, and (5) antibody-dependent cytotoxicity ofinfected cells (Pierson et al., 2008 Cell Host & Microbe 4:229-38).Flavivirus neutralization is thought to require binding by multipleantibodies (Dowd et al., 2011 Virology 411:306-15). Studies with E16, anEDIII binding mAb that neutralizes West Nile virus at a post attachmentstage, indicate that ˜30 antibodies need to bind for effectiveneutralization. Studies have suggested that both the affinity ofantibody binding and the total number of accessible epitopes contributeto the neutralization potency of an antibody. Thus, even for an antibodythat binds with high affinity, the antibody will fail to neutralize ifthe number of accessible epitopes is below certain level required forneutralization. Conversely, a lower affinity antibody may neutralize ifmany of the epitopes are accessible to binding.

As already noted, Dengue viruses (DVs) display antibody epitopes thatare unique to each serotype and epitopes that are shared betweenserotypes. Most studies to understand how antibodies neutralize orenhance DV have been done with mouse monoclonal antibodies (mAbs). As Eprotein is the main antigen exposed on the surface of the virion, mousemAbs that bind to E protein have been the focus of much analysis.Although neutralizing mouse mAbs have been mapped to all three domains,the most strongly neutralizing mAbs are serotype-specific and bind toEDIII, which protrudes from the surface of the virion. Two partiallyoverlapping epitopes on EDIII designated the lateral ridge and A-strandepitopes are the main targets of mouse mAbs that neutralize DV.

The lateral ridge epitope interacts with serotype-specific stronglyneutralizing antibodies. For example, mAb 3H5 maps to the EDIII-LR of DVserotype 2, and the epitope recognized by these mAbs is located on boththe A-strand (amino acid 304) and the FG loop (residues 383 and 384)(Sukupolvi-Petty et al., 2007 Journal of Virology 81(23): 12816-12826).

However, not all antibodies that bind EDIII exhibit type-specificneutralizing activity. mAbs that bind to the A-strand epitope crossreact with more than one serotype of DV and are designated Dengue Virussub-complex neutralizing mAbs. For example, the sub complex-specific mAb1A1D-2 recognizes an epitope centered on the A-strand of the lateralsurface of EDIII and can neutralize infection by DV serotypes 1-3(DV1-3), but not DV serotype 4 (DV4) (Lok et al., 2008 Nature Struct MolBiol 15(3):312-317; Roehrig et al., 1998 Virology 246(2):317-328;Sukupolvi-Petty et al., 2007 Journal of Virology 81(23): 12816-12826).The molecular basis for the specificity of this mAb has beeninvestigated; only one of three residues at the center of the 1A1D-2epitope is conserved among all four DV serotypes (DV1-4). A similarA-strand epitope is also recognized by the broadly neutralizing crossreactive DV mAb 4E11 (Thullier et al., 2001 Journal Gen Virol.82(8):1885-1892). Experimental approaches so far have however, failed toyield antibodies capable of potently neutralizing all four DV serotypes.

One particular murine monoclonal antibody, known as 4E11, that bindswithin EDIII of the E glycoprotein, shows potent neutralizing activityagainst DV serotypes 1-4. 4E11 binds to a conformational epitope on DVEDIII of E glycoprotein and cross reacts with all four serotypes. 4E11potently neutralizes DV1-3 by interfering with attachment to host cell.However, it has poor affinity, and therefore weak neutralizing activity,against DV4

A hybridoma cell line that secretes mouse monoclonal antibody 4E11 hasbeen deposited in the American Type Culture Collection (ATCC) Accessionnumber: HB-9259. Sequences of wild type (“wt”) 4E11 heavy chain (HC; SEQID NO. 1) and light chain (LC; SEQ ID NO. 2) are known. Sequences of wt4E11 framework (FR) and complement determining regions (CDRs) are known(wt 4E11 HC FR1 is SEQ ID NO. 3, wt 4E11 HC FR2 is SEQ ID NO. 4, wt 4E11HC FR3 is SEQ ID NO. 5, wt 4E11 HC FR4 is SEQ ID NO. 6, wt 4E11 HC CDR1is SEQ ID NO. 7, wt 4E11 HC CDR2 is SEQ ID NO. 8, wt 4E11 HC CDR3 is SEQID NO. 9; wt 4E11 LC FR1 is SEQ ID NO. 10, wt 4E11 LC FR2 is SEQ ID NO.11, wt 4E11 LC FR3 is SEQ ID NO. 12, wt 4E11 LC FR4 is SEQ ID NO. 13, wt4E11 LC CDR1 is SEQ ID NO. 14, wt 4E11 LC CDR2 is SEQ ID NO. 15, wt 4E11LC CDR3 is SEQ ID NO. 16).

SEQ ID NO. 1: EVKLLEQSGAELVKPGASVRLSCTASGFNIKDTYMSWVKQRPEQGLEWIGRIDPANGDTKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYCSRGWEGFAYWGQGTLVTVSA SEQ ID NO. 2:ELVMTQTPASLAVSLGQRATISCRASENVDRYGNSFMHWYQQKAGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVA TYFCQRSNEVPWTFGGGTKLEIKRSEQ ID NO. 3: EVKLLEQSGAELVKPGASVRLSCTAS SEQ ID NO. 4:YMSWVKQRPEQGLEWIGRI SEQ ID NO. 5:TKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYCSR SEQ ID NO. 6: WGQGTLVTVSASEQ ID NO. 7: GFNIKDT SEQ ID NO. 8: DPANGD SEQ ID NO. 9: GWEGFAYSEQ ID NO. 10: ELVMTQTPASLAVSLGQRATISC SEQ ID NO. 11: WYQQKAGQPPKLLIYSEQ ID NO. 12: GIPARFSGSGSRTDFTLTINPVEADDVATYFC SEQ ID NO. 13:FGGGTKLEIKR SEQ ID NO. 14: RASENVDRYGNSFMH SEQ ID NO. 15: RASNLESSEQ ID NO. 16: QRSNEVPWT

The present invention encompasses the recognition that it would bedesirable to develop antibodies (or other antibody agents) that arevariants of wt 4E11. The present invention particularly provides suchantibodies and antibody agents. That is, the present invention providesvarious antibody agents that show significant structural identity with4E11 and moreover show improved functional characteristics (e.g.,neutralization of DV4) as compared with that observed with wt 4E11.

The present disclosure provides a novel scoring metric for docking anantigen-antibody interaction. The scoring metric framework ranksprotein-protein interfaces according to physicochemical features andpropensities of pairwise amino acid interactions observed inintermolecular interfaces. The present disclosure uses this framework tomodify properties of an existing antibody. In some embodiments, thespecificity and affinity of an antibody for its antigen is modified. Insome embodiments, the modified antibody is a monoclonal antibody. Insome embodiments, the framework disclosed in the present invention isused to engineer broader specificity and affinity to an anti-DVneutralizing mAb.

Using the docked model, the mode of anti-DV antibodies binding to allfour serotypes of DV (DV1-4) was examined and the structural basis ofpoor affinity of these antibodies towards DV4 were identified. Mutationswere carefully designed on the paratope of these antibodies to improvetheir affinity, and thereby their neutralizing activity, towards DV4,while maintaining affinity and neutralizing activity towards DV1-3. Fordesigning the mutations, the CDR loop residues of the mAbs werecarefully examined one at a time. At a given CDR position, the“wild-type” residue was systematically substituted by the remainingamino acids excluding glycine (Gly) and proline (Pro), and theprobability of replacement was evaluated at each instance using thestatistical pairwise propensities. Gly and Pro residues were notmodified to avoid alteration in the backbone conformation. Singlemutations with high replacement potential were modeled, and re-evaluatedcomputationally to find mutations that: (1) do not alter phi-psi values;(2) do not bury polar groups; and (3) improved H-bonds, salt bridge, vander Waals, hydrophobic contacts, and packing. Promising single mutationsidentified by the computational approach were screened using a highthroughput indirect enzyme linked immunosorbent assay (ELISA) method toidentify positive mutations that improve affinity towards DV4 EDIIIwhile maintaining affinity towards DV1-3 EDIII. Finally, positive singlemutations were combined to rationally design high affinity antibodies.Competition ELISA experiments were carried out to determine theaffinity, at equilibrium and in solution, between the engineeredantibodies and EDIII from each of the four serotypes. Bindingmeasurements were verified using surface plasmon resonance (SPR)analysis.

In some embodiments, antibodies against A-strand epitope can beengineered to bind to all four serotypes of DV. In some embodiments, wt4E11 anti-DVantibody is modified to improve its affinity, and therebyneutralizing activity towards DV4, while maintaining affinity towardsDV1-3. In some embodiments, one of the engineered antibodies displays˜15 and ˜450 fold improvement in affinity toward EDIII of DV2 and DV4,respectively, while maintaining original affinity towards EDIII of DV1and DV3. In some embodiments, compared to wt mAb 4E11, the engineeredantibody showed >75 fold increased neutralizing potential towards DV4,while still maintaining “wild-type” activity towards other serotypes.The engineered 4E11 antibody according to the present inventionrepresents an interesting candidate for a therapeutic antibody to treatDengue disease.

Antibody 4E5A

One particular murine monoclonal antibody, known as 4E5A, that bindswithin EDIII of the E glycoprotein, shows potent neutralizing activityagainst DV serotypes 1-4. 4E5A binds to a conformational epitope on DVEDIII of E glycoprotein and cross reacts with all four serotypes. 4E5Apotently neutralizes DVI-4 by interfering with attachment to host cell.

4E5A has five mutations, four in the light chain (VL) and one in theheavy chain (VH) compared to the predecessor antibody E411. Sequences of4E5A framework (FR) and complement determining regions (CDRs) arepresented below (4E5A HC FR1 is SEQ ID NO. 31, 4E5A HC FR2 is SEQ ID NO.32, 4E5A HC FR3 is SEQ ID NO. 33, 4E5A HC FR4 is SEQ ID NO. 34, 4E5A HCCDR1 is SEQ ID NO. 35, 4E5A HC CDR2 is SEQ ID NO. 36, 4E5A HC CDR3 isSEQ ID NO. 37; 4E5A LC FR1 is SEQ ID NO. 38, 4E5A LC FR2 is SEQ ID NO.39, 4E5A LC FR3 is SEQ ID NO. 40, 4E5A LC FR4 is SEQ ID NO. 41, 4E5A LCCDR1 is SEQ ID NO. 42, 4E5A LC CDR2 is SEQ ID NO. 43, 4E5A LC CDR3 isSEQ ID NO. 44).

SEQ ID NO. 29: EVKLLEQSGAELVKPGASVRLSCTASGFNIKDTYMSWVKQRPEQGLEWIGRIDPENGDTKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYCSRGWEGFAYWGQGTLVTVSA SEQ ID NO. 30:ELVMTQTPASLAVSLGQRATISCRASENVDKYGNSFMHWYQQKAGQPPKLLIYRASELQWGIPARFSGSGSRTDFTLTINPVEADDVA TYFCQRSNEVPWTFGGGTKLEIKRSEQ ID NO. 31: EVKLLEQSGAELVKPGASVRLSCTAS SEQ ID NO. 32:YMSWVKQRPEQGLEWIGRI SEQ ID NO. 33:TKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYCSR SEQ ID NO. 34: WGQGTLVTVSASEQ ID NO. 35: GFNIKDT SEQ ID NO. 36: DPENGD SEQ ID NO. 37: GWEGFAYSEQ ID NO. 38: ELVMTQTPASLAVSLGQRATISC SEQ ID NO. 39: WYQQKAGQPPKLLIYSEQ ID NO. 40: GIPARFSGSGSRTDFTLTINPVEADDVATYFC SEQ ID NO. 41:FGGGTKLEIKR SEQ ID NO. 42: RASENVDKYGNSFMH SEQ ID NO. 43: RASELQWSEQ ID NO. 44: QRSNEVPWT

The present invention encompasses the recognition that it would bedesirable to develop antibodies (or other antibody agents) that arevariants of wt 4E5A. The present invention particularly provides suchantibodies and antibody agents. That is, the present invention providesvarious antibody agents that show significant structural identity with4E5A and moreover show improved functional characteristics (e.g.,binding and neutralization of DV4) as compared with that observed withwt 4E5A.

Using the docked model described in the section above, the mode ofanti-DV antibodies binding to all four serotypes of DV (DV1-4) wasexamined and the structural basis of poor affinity of these antibodiestowards DV4 were identified. Mutations were carefully designed on theparatope of these antibodies to improve their affinity, and therebytheir neutralizing activity, towards DV4, while maintaining affinity andneutralizing activity towards DV1-3. For designing the mutations, theCDR loop residues of the mAbs were carefully examined one at a time. Ata given CDR position, the “wild-type” residue was systematicallysubstituted by the remaining amino acids excluding glycine (Gly) andproline (Pro), and the probability of replacement was evaluated at eachinstance using the statistical pairwise propensities. Gly and Proresidues were not modified to avoid alteration in the backboneconformation. Single mutations with high replacement potential weremodeled, and re-evaluated computationally to find mutations that: (1) donot alter phi-psi values; (2) do not bury polar groups; and (3) improvedH-bonds, salt bridge, van der Waals, hydrophobic contacts, and packing.Promising single mutations identified by the computational approach werescreened using a high throughput indirect enzyme linked immunosorbentassay (ELISA) method to identify positive mutations that improveaffinity towards DV4 EDIII while maintaining affinity towards DV1-3EDIII. Finally, positive single mutations were combined to rationallydesign high affinity antibodies. Competition ELISA experiments werecarried out to determine the affinity, at equilibrium and in solution,between the engineered antibodies and EDIII from each of the fourserotypes. Binding measurements were verified using surface plasmonresonance (SPR) analysis.

In some embodiments, antibodies against A-strand epitope can beengineered to bind to all four serotypes of DV. In some embodiments, wt4E5A anti-DVantibody is modified to improve its affinity, and therebyneutralizing activity towards DV4, while maintaining affinity towardsDV1-3. In some embodiments, one of the engineered antibodies displays˜8.75 fold improvement in affinity toward EDIII of DV4, whilemaintaining (or improving) original affinity towards EDIII of DV1, DV2and DV3. The engineered 4E5A antibodies according to the presentinvention represents interesting candidates for therapeutic antibodiesto treat Dengue disease.

Provided Variant DV Antibody Agents

It will be appreciated that provided antibody agents may be engineered,produced, and/or purified in such a way as to improve characteristicsand/or activity of the antibody agents. For example, improvedcharacteristics of provided antibody agents include, but are not limitedto, increased stability, improved binding affinity and/or avidity,increased binding specificity, increased production, decreasedaggregation, decreased nonspecific binding, among others.

In general, as described herein, provided antibody agents can be orinclude, e.g., a polyclonal antibody; a monoclonal antibody or antigenbinding fragment thereof, a modified antibody such as a chimericantibody, reshaped antibody, humanized antibody, or fragment thereof(e.g., Fab′, Fab, F(ab′)2); or a biosynthetic antibody, e.g., a singlechain antibody, single domain antibody (DAB), Fv, single chain Fv(scFv), or the like.

Methods of making and using polyclonal and monoclonal antibodies aredescribed, e.g., in Harlow et al., Using Antibodies: A LaboratoryManual: Portable Protocol I. Cold Spring Harbor Laboratory (Dec. 1,1998). Methods for making modified antibody agents, such as, antibodiesand antibody fragments (e.g., chimeric antibodies, reshaped antibodies,humanized antibodies, or fragments thereof, e.g., Fab′, Fab, F(ab′)2fragments); or biosynthetic antibodies (e.g., single chain antibodies,single domain antibodies (DABs), Fv, single chain Fv (scFv), and thelike), are known in the art and can be found, e.g., in Zola, MonoclonalAntibodies: Preparation and Use of Monoclonal Antibodies and EngineeredAntibody Derivatives, Springer Verlag (Dec. 15, 2000; 1st edition).

The present invention provides antibody agents that bind to all fourserotypes of DV (DV1-4). In some embodiments, the present inventionprovides antibody agents that bind to DV1 with a higher affinity, ascompared to the affinity of another antibody to DV1. In someembodiments, the present invention provides antibody agents that bindwith a higher affinity to DV2, as compared to the affinity of anotherantibody to DV2. In some embodiments, the present invention providesantibody agents that bind with a higher affinity to DV3, as compared tothe affinity of another antibody to DV3. In some embodiments, thepresent invention provides antibody agents that bind with a higheraffinity to DV4, as compared to the affinity of another antibody to DV4.In some embodiments, the present invention provides antibody agents thatbind with a higher affinity to DV1, DV2, DV3, and DV4, as compared tothe affinity of another antibody to DV1, DV2, DV3, and DV4. In someembodiments, the present invention provides antibody agents that bindwith higher affinity to DV4, and retain binding affinity to DV1, DV2,and DV3, as compared to the affinities of another antibody for these DVserotypes. In some embodiments, the present invention provides antibodyagents that bind to DV1 and DV4 with higher affinities, as compared tothe affinities of another antibody for these DV serotypes. In someembodiments, provided antibody agents bind with a higher affinity to DV1and DV4, and retain their binding affinity to DV2 and DV3, as comparedto the affinities of another antibody for these DV serotypes. In someembodiments, the present invention provides antibody agents that bind toDV2 and DV4 with higher affinities, as compared to the affinities ofanother antibody for these DV serotypes. In some embodiments, providedantibody agents bind with a higher affinity to DV2 and DV4, and retaintheir binding affinity to DV1 and DV3, as compared to the affinities ofanother antibody for these DV serotypes. In some embodiments, thepresent invention provides antibody agents that bind to DV3 and DV4 withhigher affinities, as compared to the affinities of another antibody forthese DV serotypes. In some embodiments, provided antibody agents bindwith a higher affinity to DV3 and DV4, and retain their binding affinityto DV1 and DV2, as compared to the affinities of another antibody forthese DV serotypes.

In some embodiments, provided antibody agents bind to one or more ofDV1-4 with an affinity of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or more than theaffinity of a different antibody for one or more of DV1-4. In someembodiments, provided antibody agents bind to one or more of DV1-4 withan affinity of at least 2-fold, at least 5-fold, at least 10-fold, atleast 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, atleast 60-fold, at least 70-fold, at least 80-fold, at least 90-fold, atleast 100-fold, at least 200-fold, at least 300-fold, at least 400-fold,at least 500-fold or greater affinity than that of a different antibodyfor one or more of DV1-4. In some embodiments, provided antibody agentsshow binding affinities for different DV serotypes that are within 2,within 5, within 10, within 25, within 50, within 100, within 150,within 200, within 250, within 300, within 350, or within 400-foldaffinity of one another.

In some embodiments, provided antibody agents show a neutralization IC₅₀(ug/ml) within a range as described and/or exemplified herein. In someembodiments, provided antibody agents show a neutralization IC₅₀ (ug/ml)whose lower bound is about 0.05 ug/ml and upper bound is about 10 ug/ml.In some embodiments, provided antibody agents show a neutralization IC₅₀(ug/ml) whose lower bound is selected from the group consisting of 0.05ug/ml, 0.1 ug/ml, 0.2 ug/ml, 0.3 ug/ml, 0.4 ug/ml, 0.5 ug/ml, 0.6 ug/ml,0.7 ug/ml, 0.8 ug/ml, 0.9 ug/ml, 1.0 ug/ml, 1.1 ug/ml, 1.2 ug/ml, 1.3ug/ml, 1.4 ug/ml, 1.5 ug/ml, 1.6 ug/ml, 1.7 ug/ml, 1.8 ug/ml, 1.9 ug/ml,2.0 ug/ml, 2.5 ug/ml, 3.0 ug/ml, 3.5 ug/ml, 4.0 ug/ml, 4.5 ug/ml, 5.0ug/ml or more, and whose upper bound is higher than the lower bound andis selected from the group consisting of 1.5 ug/ml, 1.6 ug/ml, 1.7ug/ml, 1.8 ug/ml, 1.9 ug/ml, 2.0 ug/ml, 2.5 ug/ml, 3.0 ug/ml, 3.5 ug/ml,4.0 ug/ml, 4.5 ug/ml, 5.0 ug/ml, 5.5 ug/ml, 6.0 ug/ml, 6.5 ug/ml, 7.0ug/ml, 7.5 ug/ml, 8.0 ug/ml, 8.5 ug/ml, 9.0 ug/ml, 9.5 ug/ml, 10.0 ug/mlor more.

In some embodiments, provided antibody agents show binding to DV1-4 witha KD (nM) less than 40000 nM, less than 30000 nM, less than 20000 nM,less than 10000 nM, less than 5000 nM, less than 2000 nM, less than 1500nM, less than 1000 nM, less than 500 nM, less than 250 nM, less than 225nM, less than 200 nM, less than 175 nM, less than 150 nM, less than 125nM, less than 100 nM, less than 75 nM, less than 50 nM, less than 25 nM,less than 15 nM, less than 10 nM, less than 5 nM, less than 2.5 nM, lessthan 1 nM, less than 0.5 nM, less than 0.25 nM, less than 0.1 nM.

In some embodiments, provided antibody agents show binding to DV1-4 witha K_(on)(M⁻¹s⁻¹) whose lower bound is about 0.01×10⁵ M⁻¹s⁻¹ and upperbound is about 5.0×10⁶ M⁻¹s⁻¹. In some embodiments, provided antibodiesshow binding to DV1-4 with a K_(on)(M⁻¹s⁻¹) whose lower bound isselected from the group consisting of 0.01×10⁵ M⁻¹s⁻¹, 0.05×10⁵ M⁻¹s⁻¹,0.1×10⁵ M⁻¹s⁻¹, 0.5×10⁵ M⁻¹s⁻¹, 1.0×10⁵ M⁻¹s⁻¹, 2.0×10⁵ M⁻¹s⁻¹, 5.0×10⁵M⁻¹s⁻¹, 7.0×10⁵ M⁻¹s⁻¹, or more, and whose upper bound is higher thanthe lower bound and is selected from the group consisting of 1.0×10⁶M⁻¹s⁻¹, 1.5×10⁶ M⁻¹s⁻¹, 2.0×10⁶ M⁻¹s⁻¹, 2.5×10⁶ M⁻¹s⁻¹, 3.0×10⁶ M⁻¹s⁻¹,3.5×10⁶ M⁻¹s⁻¹, 4.0×10⁶ M⁻¹s⁻¹, 4.5×10⁶ M⁻¹s⁻¹, 5.0×10⁶ M⁻¹s⁻¹, or more.

In some embodiments, provided antibody agents show binding to DV1-4 witha K_(off) (s⁻¹) whose lower bound is about 5×10⁻⁴ s⁻¹ and upper bound isabout 900×10⁻⁴ s⁻¹. In some embodiments, provided antibody agents showbinding to DV1-4 with a K_(off) (s⁻¹) whose lower bound is selected fromthe group consisting of 5×10⁻⁴ s⁻¹, 10×10⁻⁴ s⁻¹, 12×10⁻⁴ s⁻¹, 13×10⁻⁴s⁻¹, 14×10⁻⁴ s⁻¹, 15×10⁻⁴ s⁻¹, 18×10⁻⁴ s⁻¹, 20×10⁻⁴ s⁻¹, or more, andwhose upper bound is higher than the lower bound and is selected fromthe group consisting of 50×10⁻⁴ s⁻¹, 100×10⁻⁴ s⁻¹, 120×10⁻⁴ s⁻¹,140×10⁻⁴ s⁻¹, 150×10⁻⁴ s⁻¹, 200×10⁻⁴ s⁻¹, 300×10⁻⁴ s⁻¹, 400×10⁻⁴ s⁻¹,500×10⁻⁴ s⁻¹, 600×10⁻⁴ s⁻¹, 700×10⁻⁴ s⁻¹, 800×10⁻⁴ s⁻¹, 900×10⁻⁴ S1, ormore.

In some embodiments, provided antibody agents bind to E glycoprotein ofDV1-4. In certain embodiments, provided antibody agents bind to EDIII ofDV1-4 (SEQ ID NOs. 17-20). In some embodiments, provided antibody agentsbind to A-strand of DV1-4. In some embodiments, the present inventionprovides antibody agents that bind with higher affinity to EDIII of DV4(SEQ ID NO. 20). In some embodiments, the present invention providesantibody agents that bind with higher affinity to A-strand of DV4.

SEQ ID NO. 17: MCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALK LSWFK SEQ ID NO. 18:MCTGKFKVVKEIAETQHGTMVIRVQYEGDDSPCKIPFEIMDLEKKHVLGRLITVNPIVIEKDSPINIEAEPPFGDSYIIIGVEPGQLK LNWFK SEQ ID NO. 19:MCTNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDNALKIN WYK SEQ ID NO. 20:MCSGKFSIDKEMAETQHGTTVVKVKYEGAGAPCKVPIEIRDVNKEKVVGRIISSTPLAENTNSVTNIELEPPFGDSYIVIGVGNSALTLH WFR

In some embodiments, provided antibody agents bind to E glycoprotein ofDV1-4. In certain embodiments, provided antibody agents bind to EDIII ofDV1-4 (SEQ ID NOs. 17-20). In some embodiments, provided antibody agentsbind to A-strand of DV1-4. In some embodiments, the present inventionprovides antibody agents that bind with higher affinity to EDIII of DV4(SEQ ID NO. 20). In some embodiments, the present invention providesantibody agents that bind with higher affinity to A-strand of DV4.

In some embodiments, the present invention identifies antibody agentsthat bind to one or more amino acid residues in EDIII of DV1-4 (SEQ IDNOs. 17-20) at positions 305, 306, 307, 308, 309, 310, 311, 312, 323,325, 327, 329, 360, 361, 362, 363, 364, 385, 387, 388, 389, 390, 391,and/or combinations thereof. In some embodiments, the present inventionidentifies antibody agents that bind to one or more amino acid residuesin EDIII of DV1-4 (SEQ ID NOs. 17-20) at positions 305, 310, 311, 323,327, 329, and/or combinations thereof. In some embodiments, the presentinvention identifies antibody agents that bind amino acid residues inEDIII of DV1-4 (SEQ ID NOs. 17-20) at positions 305, 310, 311, 323, 327,and 329. In some embodiments, the present invention identifies antibodyagents that bind amino acid residue in EDIII of DV1-4 (SEQ ID NOs.17-20) at position 305. In some embodiments, the present inventionidentifies antibody agents that bind amino acid residue in EDIII ofDV1-4 (SEQ ID NOs. 17-20) at position 310. In certain embodiments, thepresent invention identifies antibody agents that bind amino acidresidue in EDIII of DV1-4 (SEQ ID NOs. 17-20) at position 311. In someembodiments, the present invention identifies antibody agents that bindamino acid residue in EDIII of DV1-4 (SEQ ID NOs. 17-20) at position323. In some embodiments, the present invention identifies antibodyagents that bind amino acid residue in EDIII of DV1-4 (SEQ ID NOs.17-20) at position 327. In some embodiments, the present inventionidentifies antibody agents that bind amino acid residue in EDIII ofDV1-4 (SEQ ID NOs. 17-20) at position 329.

In some embodiments, a serine, lysine, and/or threonine residue atposition 305 contribute(s) to binding to provided antibody agents. Insome embodiments, a lysine residue at position 310 contributes tobinding to provided antibody agents. In some embodiments, a lysineresidue at position 311 contributes to binding to provided antibodyagents. In some embodiments, an arginine, lysine, and/or glutamineresidue at position 323 contribute(s) to binding to provided antibodyagents. In some embodiments, a serine and/or glutamate residue atposition 327 contribute(s) to binding to provided antibody agents. Insome embodiments, an arginine, aspartate, and/or glutamate residue atposition 329 contribute(s) to binding to provided antibody agents.

In some embodiments, the present invention provides antibody agents thatbind with higher affinity to DV1, as compared to a wild type (“wt”) DVantibody. In some embodiments, the present invention provides antibodyagents that bind with higher affinity to DV2, as compared to a wt orparent reference DV antibody. In some embodiments, the present inventionprovides antibody agents that bind with higher affinity to DV3, ascompared to a reference antibody such as a wt DV antibody. In someembodiments, the present invention provides antibody agents that bindwith higher affinity to DV4, as compared to a reference DV antibody. Insome embodiments, the present invention provides antibody agents thatbind with higher affinity to DV1, DV2, DV3, and DV4, as compared to areference DV antibody. In some embodiments, the present inventionprovides antibody agents that bind with higher affinity to DV4 andretain binding affinity to DV1, DV2, and DV3, as compared to a referenceDV antibody. In some embodiments, the present invention providesantibody agents that bind with higher affinity to DV2 and DV4, ascompared to a reference (wt) DV antibody. In some embodiments, providedantibody agents that bind with higher affinity to DV2 and DV4 and retaintheir binding affinity to DV1 and DV3, as compared to a reference DVantibody. In some embodiments, a wt DV antibody is a wt 4E11 antibody.

As described herein, the present invention provides antibody agents thatshow certain structural (i.e., sequence) relationship with 4E11 and/orhave particular functional attributes, including, for example, certainimproved functional attributes as compared with wt 4E11.

The present invention also provides antibody agents that show certainstructural (i.e., sequence) relationship with 4E5A and/or haveparticular functional attributes, including, for example, certainimproved functional attributes as compared with 4E5A.

In some embodiments, the present invention provides antibody agentswhose amino acid sequences, show specified levels of homology and/oridentity with wt 4E11. In some embodiments provided antibody agents showat least 60%, at least 70%, at least 80%, at least 90%, at least 95%, atleast 99% identity with wt 4E11 (i.e., with SEQ ID NOs. 1-2).

In some embodiments, provided antibody agents have a heavy chain (HC;SEQ ID NO. 21) CDR1 comprising sequence GFNIKDT (SEQ ID NO. 23), a HCCDR2 comprising sequence DPENGD (SEQ ID NO. 24), a HC CDR3 comprisingsequence GWEGFAY (SEQ ID NO. 25), a light chain (LC; SEQ ID NO. 22) CDR1comprising sequence RASENVDKYGNSFMH (SEQ ID NO. 26), a LC CDR2 regioncomprising sequence RASELQW (SEQ ID NO. 27) and a LC CDR3 regioncomprising sequence QRSNEVPWT (SEQ ID NO. 28).

SEQ ID NO. 21: EVKLLEQSGAELVKPGASVRLSCTASGFNIKDTYMSWVKQRPEQGLEWIGRIDPENGDTKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYY CSRGWEGFAYWGQGTLVTVSASEQ ID NO. 22: ELVMTQTPASLAVSLGQRATISCRASENVDKYGNSFMHWYQQKAGQPPKLLIYRASELQWGIPARFSGSGSRTDFTLTINPVEADDVATYFCQRSN EVPWTFGGGTKLEIKR

In some embodiments, the present invention provides antibody agentswhose amino acid sequences, show specified levels of homology and/oridentity with 4E5A. In some embodiments provided antibody agents show atleast 60%, at least 70%, at least 80%, at least 90%, at least 95%, atleast 99% identity with 4E5A (i.e., with SEQ ID NOs. 29-30).

In some embodiments, provided antibody agents have a heavy chain (HC;SEQ ID NO. 29) CDR1 comprising sequence GFNIKDT (SEQ ID NO. 35), a HCCDR2 comprising sequence DPENGD (SEQ ID NO. 36), a HC CDR3 comprisingsequence GWEGFAY (SEQ ID NO. 37), a light chain (LC; SEQ ID NO. 30) CDR1comprising sequence RASENVDKYGNSFMH (SEQ ID NO. 42), a LC CDR2 regioncomprising sequence RASELQW (SEQ ID NO. 43) and a LC CDR3 regioncomprising sequence QRSNEVPWT (SEQ ID NO. 44).

SEQ ID NO. 29: EVKLLEQSGAELVKPGASVRLSCTASGFNIKDTYMSWVKQRPEQGLEWIGRIDPENGDTKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAV YYCSRGWEGFAYWGQGTLVTVSASEQ ID NO. 30: ELVMTQTPASLAVSLGQRATISCRASENVDKYGNSFMHWYQQKAGQPPKLLIYRASELQWGIPARFSGSGSRTDFTLTINPVEADDVATYFCQR SNEVPWTFGGGTKLEIKR

In some embodiments, provided antibody agents have one or more CDRsand/or one or more FRs that are identical in sequence to a correspondingCDR or FR of wt 4E11 (i.e. to one or more of SEQ ID NOs. 7-9, 14-16 or3-6, 10-13). In some embodiments, provided antibody agents have one ormore CDRs and/or FRs showing a specified degree of homology and/oridentity with the corresponding CDRs and/or FRs of wt 4E11 as discussedbelow. In some embodiments, all CDRs and FRs of a provided antibodyagents show at least the specified level of homology and/or identity. Insome embodiments, a provided antibody agents has CDR and FR sequencesthat together contain no more than 18, 17, 16, 15, 14, 13, 12, 11, 10,9, 8, 7, 6, 5, 4, 3, 2, or 1 substitutions as compared with wt 4E11.

In some embodiments, a complementarity determining region (CDR) 1 of anantibody agent of the present invention shows at least 65%, more than70%, more than 75%, more than 80%, more than 85%, more than 90%, morethan 95%, or more than 99% identity with wt 4E11 (SEQ ID NO. 7 and SEQID NO. 14). In some embodiments, a provided CDR1 has an amino acidsequence that is identical to that of wt 4E11 and/or does not containany amino acid substitutions as compared with CDR1 of wt 4E11 (SEQ IDNO. 7 and SEQ ID NO. 14). In some embodiments, a provided CDR1 has oneor more amino acid substitutions as compared to wt 4E11 (SEQ ID NO. 7and SEQ ID NO. 14). In some embodiments, a provided CDR1 will have twoor more amino acid substitutions as compared to wt 4E11 (SEQ ID NO. 7and SEQ ID NO. 14). In some embodiments, a provided CDR has 1, 2, 3, 4or 5 substitutions and in some embodiments 1, 2, or 3 substitutions ascompared with wt 4E11.

In some embodiments, a CDR2 of an antibody agent of the presentinvention shows at least 65%, more than 70%, more than 75%, more than80%, more than 85%, more than 90%, more than 95%, or more than 99%identity with wt 4E11 (SEQ ID NO. 8 and SEQ ID NO. 15). In someembodiments, a provided CDR2 has an amino acid sequence that isidentical to that of wt 4E11 and/or does not contain any amino acidsubstitutions as compared with CDR2 of wt 4E11 (SEQ ID NO. 8 and SEQ IDNO. 15). In some embodiments, a provided CDR2 has one or more amino acidsubstitutions as compared to wt 4E11 (SEQ ID NO. 8 and SEQ ID NO. 15).In some embodiments, a provided CDR2 will have two or more amino acidsubstitutions as compared to wt 4E11 (SEQ ID NO. 8 and SEQ ID NO. 15).In some embodiments, a provided CDR has 1, 2, 3, 4 or 5 substitutionsand in some embodiments 1, 2, or 3 substitutions as compared with wt4E11.

In some embodiments, a CDR3 of an antibody agent of the presentinvention shows at least 65%, more than 70%, more than 75%, more than80%, more than 85%, more than 90%, more than 95%, or more than 99%identity with wt 4E11 (SEQ ID NO. 9 and SEQ ID NO. 16). In someembodiments, a provided CDR3 has an amino acid sequence that isidentical to that of wt 4E11 and/or does not contain any amino acidsubstitutions as compared with CDR3 of wt 4E11 (SEQ ID NO. 9 and SEQ IDNO. 16). In some embodiments, a provided CDR3 has one or more amino acidsubstitutions as compared to wt 4E11 (SEQ ID NO. 9 and SEQ ID NO. 16).In some embodiments, a provided CDR3 will have two or more amino acidsubstitutions as compared to wt 4E11 (SEQ ID NO. 9 and SEQ ID NO. 16).In some embodiments, a provided CDR has 1, 2, 3, 4 or 5 substitutionsand in some embodiments 1, 2, or 3 substitutions as compared with wt4E11.

In some embodiments, a provided framework region 1 (FR1) of an antibodyagent of the present invention will share more than 65%, more than 70%,more than 75%, more than 80%, more than 85%, more than 90%, more than95%, or more than 99% percent identity with wt 4E11 (SEQ ID ID NO. 3 andSEQ ID NO. 10). In some embodiments, a provided FR1 will not have anamino acid substitution as compared to wt 4E11 (SEQ ID ID NO. 3 and SEQID NO. 10). In some embodiments, a provided FR1 will have one or moreamino acid substitutions as compared to wt 4E11 (SEQ ID ID NO. 3 and SEQID NO. 10). In some embodiments, a provided FR1 will have two or moreamino acid substitutions as compared to wt 4E11 (SEQ ID ID NO. 3 and SEQID NO. 10).

In some embodiments, a provided framework region 2 (FR2) of an antibodyagent of the present invention will share more than 65%, more than 70%,more than 75%, more than 80%, more than 85%, more than 90%, more than95%, or more than 99% percent identity with wt 4E11 (SEQ ID NO. 4 andSEQ ID NO. 11). In some embodiments, a provided FR2 will not have anamino acid substitution as compared to wt 4E11 (SEQ ID NO. 4 and SEQ IDNO. 11). In some embodiments, a provided FR2 will have one or more aminoacid substitutions as compared to wt 4E11 (SEQ ID NO. 4 and SEQ ID NO.11). In some embodiments, a provided FR2 will have two or more aminoacid substitutions as compared to wt 4E11 (SEQ ID NO. 4 and SEQ ID NO.11).

In some embodiments, a provided framework region 3 (FR3) of an antibodyagent of the present invention will share more than 65%, more than 70%,more than 75%, more than 80%, more than 85%, more than 90%, more than95%, or more than 99% percent identity with wt 4E11 (SEQ ID NO. 5 andSEQ ID NO. 12). In some embodiments, a provided FR3 will not have anamino acid substitution as compared to wt 4E11 (SEQ ID NO. 5 and SEQ IDNO. 12). In some embodiments, a provided FR3 will have one or more aminoacid substitutions as compared to wt 4E11 (SEQ ID NO. 5 and SEQ ID NO.12). In some embodiments, a provided FR3 will have two or more aminoacid substitutions as compared to wt 4E11 (SEQ ID NO. 5 and SEQ ID NO.12).

In some embodiments, a provided framework region 4 (FR4) of an antibodyagent of the present invention will share more than 65%, more than 70%,more than 75%, more than 80%, more than 85%, more than 90%, more than95%, or more than 99% percent identity with wt 4E11 (SEQ ID NO. 6 andSEQ ID NO. 13). In some embodiments, a provided FR4 will not have anamino acid substitution as compared to wt 4E11 (SEQ ID NO. 6 and SEQ IDNO. 13). In some embodiments, a provided FR4 will have one or more aminoacid substitutions as compared to wt 4E11 (SEQ ID NO. 6 and SEQ ID NO.13). In some embodiments, a provided FR3 will have two or more aminoacid substitutions as compared to wt 4E11 (SEQ ID NO. 6 and SEQ ID NO.13).

In some embodiments, the VH CDR of the provided antibody agents show atleast 60%, at least 70%, at least 80%, at least 90%, at least 95%, atleast 99% identity with wt 4E11 (SEQ ID NOs.: 7-9). In some embodiments,the VH CDR of the provided antibody agents show at least 60%, at least70%, at least 80%, at least 90%, at least 95%, at least 99% identitywith wt 4E11 (SEQ ID NOs.: 7-9), but differs by substitution of at leastone amino acid substitution within the CDR. In some embodiments, the VHCDR of provided antibody agents have a substitution of the correspondingamino acid residue at position 55 of the wt 4E11 antibody. In someembodiments, a substitute amino acid residue at position 55 is selectedfrom the group consisting of glutamate and aspartate. In someembodiments, the substitute amino acid residue at position 55 isglutamate. In some embodiments, the amino acid residue in the VH CDR ofprovided antibodies corresponding to amino acid residue at position 55of wt 4E11 is not alanine.

In some embodiments, the VL CDR of provided antibody agents show atleast 60%, at least 70%, at least 80%, at least 90%, at least 95%, atleast 99% identity with wt 4E11 (SEQ ID NOs.: 14-16). In someembodiments, the VL CDR of provided antibody agents show at least 60%,at least 70%, at least 80%, at least 90%, at least 95%, at least 99%identity with wt 4E11 (SEQ ID NOs.: 14-16), but differs by substitutionof at least one amino acid substitution within the CDR. In someembodiments, the VL CDR of provided antibody agents have one or moresubstitutions of a corresponding amino acid residue at positions 31, 57,59, 60 and/or combinations thereof, of the wt 4E11 antibody. In someembodiments, the VL CDR of provided antibody agents have a substitutionof the corresponding amino acid residue at position 31 of the wt 4E11antibody. In some embodiments, the substitute amino acid residue atposition 31 is lysine. In some embodiments, the amino acid residue inthe VL CDR of provided antibody agents corresponding to amino acidresidue at position 55 of wt 4E11 is not arginine. In some embodiments,the VL CDR of provided antibody agents have a substitution of thecorresponding amino acid residue at position 57 of the wt 4E11 antibody.In some embodiments, the substitute amino acid residue at position 57 isselected from the group consisting of glutamate and serine. In someembodiments, the substitute amino acid residue at position 57 isglutamate. In some embodiments, the amino acid residue in the VL CDR ofprovided antibody agents corresponding to amino acid residue at position57 of wt 4E11 is not asparagine. In some embodiments, the VL CDR ofprovided antibody agents have substitution of the corresponding aminoacid residue at position 59 of the wt 4E11 antibody. In someembodiments, the substitute amino acid residue at position 59 isselected from the group consisting of glutamine and asparagine. In someembodiments, the substitute amino acid residue at position 59 isglutamine. In some embodiments, the amino acid residue in the VL CDR ofprovided antibody agents corresponding to amino acid residue at position59 of wt 4E11 is not glutamate. In some embodiments, the VL CDR ofprovided antibody agents have a substitution of the corresponding aminoacid residue at position 60 of the wt 4E11 antibody. In someembodiments, the substitute amino acid residue at position 60 isselected from the group consisting of tryptophan, tyrosine, andarginine. In some embodiments, the substitute amino acid residue atposition 60 is tryptophan. In some embodiments, the amino acid residuein the VL CDR of provided antibody agents corresponding to amino acidresidue at position 60 of wt 4E11 is not serine.

In some embodiments, the VH and VL CDRs of the provided antibody agentsshow at least 60%, at least 70%, at least 80%, at least 90%, at least95%, at least 99% identity with wt 4E11 (SEQ ID NOs.: 7-9 and 14-16,respectively). In some embodiments, the VH and VL CDRs of the providedantibody agents show at least 60%, at least 70%, at least 80%, at least90%, at least 95%, at least 99% identity with wt 4E11 (SEQ ID NOs.: 7-9and 14-16, respectively), but differ by substitution of at least oneamino acid substitution within the CDRs. In some embodiments, the VH CDRof provided antibody agents have substitution of the corresponding aminoacid residue at position 55, and VL CDR of provided antibody agents havesubstitution of the corresponding amino acid residue at positions 31,57, 59 and 60, of the wt 4E11 antibody. In some embodiments, thesubstitute amino acid residue at position 55 is glutamate. In someembodiments, the substitute amino acid residue at position 31 is lysine.In some embodiments, the substitute amino acid residue at position 57 isglutamate. In some embodiments, the substitute amino acid residue atposition 59 is glutamine. In some embodiments, the substitute amino acidresidue at position 60 is tryptophan.

In some embodiments, the present invention provides antibody agents thathave a null substitution (i.e. deletion) of the amino acid residue atposition 26 relative to 4E5A. In some embodiments, the present inventionprovides antibody agents that have a null substitution (i.e. deletion)of the amino acid residue at position 27 relative to 4E5A. In someembodiments, the present invention provides antibody agents that have asubstitution of the amino acid residue at position 27 relative to 4E5A.In some embodiments, the substitute amino acid residue at position 27 isalanine.

In some embodiments, the present invention provides antibody agents thatshow binding to EDIII-DV4 (SEQ ID NO. 20) with a KD (nM) less than 40000nM, less than 30000 nM, less than 20000 nM, less than 15000 nM, lessthan 10000 nM, less than 8000 nM, less than 5000 nM, less than 4000 nM,less than 3000 nM, less than 2000 nM, less than 1500 nM, less than 1000nM, less than 500 nM, less than 250 nM, less than 225 nM, less than 200nM, less than 175 nM, less than 150 nM, less than 125 nM, less than 100nM, less than 75 nM, or less than 50 nM.

In some embodiments, the present invention provides antibody agents thatshow binding to EDIII-DV1 (SEQ ID NO. 17) with a KD (nM) of less than 3nM, less than 2.5 nM, less than 2 nM, less than 1.5 nM, less than 1.0nM, less than 0.5 nM, less than 0.4 nM, less than 0.3 nM, less than 0.2nM, less than 0.1 nM, or less than 0.05 nM.

In some embodiments, the present invention provides antibody agents thatshow binding to EDIII-DV2 (SEQ ID NO. 18) with a KD (nM) of less than 15nM, less than 12 nM, less than 10 nM, less than 8 nM, less than 7 nM,less than 5 nM, less than 2.5 nM, less than 2 nM, less than 1.5 nM, lessthan 1 nM, less than 0.5 nM, less than 0.4 nM, less than 0.3 nM, lessthan 0.2 nM, or less than 0.1 nM.

In some embodiments, the present invention provides antibody agents thatshow binding to EDIII-DV3 (SEQ ID NO. 19) with a KD (nM) of less than120 nM, less than 100 nM, less than 50 nM, less than 40 nM, less than 35nM, less than 30 nM, less than 25 nM, less than 20 nM, less than 15 nM,less than 10 nM, less than 5 nM, less than 2.5 nM, or less than 1.0 nM.

In some embodiments, the present invention provides antibody agents withat least 2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold,60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold,400-fold, 500-fold, or greater affinity for binding to EDIII-DV4 than wt4E11.

In some embodiments, the present invention provides antibody agents withat least 2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold,60-fold, 70-fold, 80-fold, 90-fold, or greater affinity for binding toEDIII-DV2 than wt 4E11.

In some embodiments, the present invention provides antibody agents withat least 1-fold, 1.5-fold, 2-fold, 5-fold, 10-fold, 20-fold, 30-fold,40-fold, 50-fold, 60-fold, or greater affinity for binding to EDIII-DV1and/or EDIII-DV3 than wt 4E11.

In some embodiments, the present invention provides antibody agents thatshow neutralization IC₅₀ (ug/ml) of EDIII-DV4 (SEQ ID NO. 20) of 60ug/ml or less, 50 ug/ml or less, 40 ug/ml or less, 30 ug/ml or less, 20ug/ml or less, 10 ug/ml or less, 5 ug/ml or less, 4 ug/ml or less, 3ug/ml or less, 2 ug/ml or less.

In some embodiments, the present invention provides antibody agents thatshow neutralization IC₅₀ (ug/ml) of EDIII-DV3 (SEQ ID NO. 19) of 7.0ug/ml or less, 6.0 ug/ml or less, 5.0 ug/ml or less, 4.0 ug/ml or less,3.0 ug/ml or less, 2.0 ug/ml or less, 1.5 ug/ml or less, 1.0 ug/ml orless, 0.90 ug/ml or less, 0.80 ug/ml or less, 0.70 ug/ml or less, 0.60ug/ml or less, 0.50 ug/ml or less.

In some embodiments, the present invention provides antibody agents thatshow neutralization IC₅₀ (ug/ml) of EDIII-DV2 (SEQ ID NO. 18) of 0.2ug/ml or less, 0.19 ug/ml or less, 0.18 ug/ml or less, 0.17 ug/ml orless, 0.16 ug/ml or less, 0.15 ug/ml or less, 0.14 ug/ml or less, 0.13ug/ml or less, 0.12 ug/ml or less, 0.11 ug/ml or less, 0.10 ug/ml orless, 0.09 ug/ml or less, 0.07 ug/ml or less, 0.06 ug/ml or less, 0.05ug/ml or less, 0.04 ug/ml or less, 0.03 ug/ml or less, 0.02 ug/ml orless, 0.01 ug/ml or less.

In some embodiments, the present invention provides antibody agents thatshow neutralization IC₅₀ (ug/ml) of EDIII-DV1 (SEQ ID NO. 17) of 5.0ug/ml or less, 4.0 ug/ml or less, 3.0 ug/ml or less, 2.5 ug/ml or less,2.0 ug/ml or less, 1.5 ug/ml or less, 1.0 ug/ml or less, 0.90 ug/ml orless, 0.70 ug/ml or less, 0.50 ug/ml or less, 0.40 ug/ml or less, 0.30ug/ml or less, 0.20 ug/ml or less, 0.10 ug/ml or less.

In some embodiments, the present invention provides antibody agents withat least 2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold,60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 150-fold, 200-fold,400-fold, 500-fold, or more reduction of IC₅₀ for neutralization ofEDIII-DV4 than wt 4E11.

In some embodiments, the present invention provides antibody agents withat least 1-fold, 1.5-fold, 2-fold, 5-fold, 10-fold, 20-fold, 30-fold,40-fold, 50-fold, 60-fold, or more reduction of IC₅₀ for neutralizationof EDIII-DV2 than wt 4E11.

In some embodiments, the present invention provides antibody agents withat least 1-fold, 1.5-fold, 2-fold, 5-fold, 10-fold, 20-fold, 30-fold,40-fold, 50-fold, 60-fold, or more reduction of IC₅₀ for neutralizationof EDIII-DV1 and/or EDIII-DV3 than wt 4E11.

In some embodiments, one or more sequences in a provided antibody agentshas been engineered (e.g., by affinity maturation or other optimizationapproach) to improve one or more characteristics or activities (e.g., toincrease stability, decrease aggregation, decrease immunogenicity, etc.)as is known in the art.

In some embodiments, an antibody agent is modified by PEGylation,methylation, sialylation, amination or sulfation. In some embodiments,an antibody agent is conjugated to an amphiphilic core/shell to producea polymeric micelle. In some embodiments, an antibody agent isconjugated to a hyperbranched macromolecule (i.e. dendrimer). In someembodiments, an antibody agent is conjugated to a natural polymerselected from the group consisting of albumin, chitosan, heparin,paclitaxel, poly-(L-glutamate), N-(2-hydroxypropyl)methacrylamide(HPMA), poly-(L-lactide) (PLA), poly(amidoamine) (PAMAM), folate and/orcombinations thereof. In some embodiments, an antibody agent comprisesone or more long unstructured tails of hydrophilic amino acids (rPEG).In some embodiments, derivatization of immunoglobulins by selectivelyintroducing sulfhydryl groups in the Fc region of an immunoglobulin,using reaction conditions that do not alter the antibody combining siteare contemplated. Antibody conjugates produced according to thismethodology may exhibit improved longevity, specificity and sensitivity(U.S. Pat. No. 5,196,066, incorporated herein by reference).Site-specific attachment of effector or reporter molecules, wherein thereporter or effector molecule is conjugated to a carbohydrate residue inthe Fc region have also been disclosed in the literature (O'Shannessy etal., 1987).

Antibodies and/or Antibody Fragments

In some embodiments, a provided DV antibody agent is or comprises anantibody or fragment thereof. In some embodiments, a provided DVantibody agent is or comprises a monoclonal antibody or fragmentthereof. In some embodiments, a provided DV antibody agent is orcomprises a polyclonal antibody or fragment thereof. In someembodiments, the DV antibody agent is or comprises a “full length”antibody, in that it contains two heavy chains and two light chains,optionally associated by disulfide bonds as occurs withnaturally-produced antibodies. In some embodiments, the DV antibodyagent is or comprises a fragment of a full-length antibody in that iscontains some, but not all of the sequences found in a full-lengthantibody. For example, in some embodiments, a DV antibody agent is orcomprises antibody fragments which include, but are not limited to, Fab,Fab′, F(ab′)2, scFv, Fv, dsFv diabody, and Fd fragments. In someembodiments, a provided DV antibody agent is or comprises an antibodythat is a member of an antibody class selected from the group consistingof IgG, IgM, IgA, IgD, IgE or fragment thereof. In some embodiments, aprovided DV antibody agent is or comprises an antibody produced bychemical synthesis. In some embodiments, a provided DV antibody agent isor comprises an antibody produced by a cell. In some embodiments, aprovided DV antibody agent is or comprises an antibody produced using arecombinant cell culture system. In some embodiments, a provided DVantibody agent is or comprises a chimeric antibody, for example frommouse, rat, horse, pig, or other species, bearing human constant and/orvariable region domains.

In some embodiments, a DV antibody agent includes one or more antibodyfragments, including, but not limited to Fab′, Fab, F(ab′)2, singledomain antibodies (DABs), Fv, scFv (single chain Fv), polypeptides withantibody CDRs, scaffolding domains that display the CDRs (e.g.,anticalins) or nanobodies. For example, a provided antibody may be a VHH(i.e., an antigen-specific VHH) antibody that comprises only a heavychain. Such antibody molecules can be derived from a llama or othercamelid antibody (e.g., a camelid IgG2 or IgG3, or a CDR-displayingframe from such camelid Ig) or from a shark antibody. In someembodiments the DV antibody agent is or comprises an avibody (diabody,tribody, tetrabody). Techniques for preparing and using variousantibody-based constructs and fragments are well known in the art. Meansfor preparing and characterizing antibodies are also well known in theart (See, e.g., Antibodies: A Laboratory Manual, Cold Spring HarborLaboratory, 1988; incorporated herein by reference).

In some embodiments, provided DV antibody agent include one or more“Mini-antibodies” or “minibodies”. Minibodies are sFv polypeptide chainswhich include oligomerization domains at their C-termini, separated fromthe sFv by a hinge region (Pack et al. (1992) Biochem 31:1579-1584). Theoligomerization domain comprises self-associating α-helices, e.g.,leucine zippers, that can be further stabilized by additional disulfidebonds. The oligomerization domain is designed to be compatible withvectorial folding across a membrane, a process thought to facilitate invivo folding of the polypeptide into a functional binding protein.Generally, minibodies are produced using recombinant methods well knownin the art. See, e.g., Pack et al. (1992) Biochem 31:1579-1584; Cumberet al. (1992) J Immunology 149B:120-126.

Antibody Agent Conjugates

In some embodiments, a provided DV antibody agent is or comprises aconjugate, in which an antibody moiety comprises or consists of theantibody or a functional portion thereof with a conjugated moiety. Insome particular embodiments, DV antibody agent as described herein areprovided and/or utilized in association with one or more active agentsor “payloads”, such as a therapeutic or detection agent. In some suchembodiments, association between the DV antibody agent and the activeagent and/or payload comprises at least one covalent interaction so thata DV antibody conjugate is provided.

In some embodiments, an antibody agent is a therapeutic payload agent isan effector entity having a desired activity, e.g., anti-viral activity,anti-inflammatory activity, cytotoxic activity, etc. Therapeutic agentscan be or comprise any class of chemical entity including, for example,proteins, carbohydrates, lipids, nucleic acids, small organic molecules,non-biological polymers, metals, ions, radioisotopes, etc. In someembodiments, therapeutic agents for use in accordance with the presentinvention may have a biological activity relevant to the treatment ofone or more symptoms or causes of DV infection (e.g., for example,anti-viral, pain-relief, anti-inflammatory, immunomodulatory,sleep-inducing activities, etc). In some embodiments, therapeutic agentsfor use in accordance with the present invention have one or more otheractivities.

In some embodiments, an antibody agent is a payload detection agent thatis or comprises any moiety which may be detected using an assay, forexample due to its specific functional properties and/or chemicalcharacteristics. Non-limiting examples of such agents include enzymes,radiolabels, haptens, fluorescent labels, phosphorescent molecules,chemiluminescent molecules, chromophores, luminescent molecules,photoaffinity molecules, colored particles or ligands, such as biotin.

Many appropriate payload detection agents are known in the art, as aresystems for their attachment to antibodies (see, for e.g., U.S. Pat.Nos. 5,021,236; 4,938,948; and 4,472,509, each incorporated herein byreference). Examples of such payload detection agents includeparamagnetic ions, radioactive isotopes, fluorochromes, NMR-detectablesubstances, X-ray imaging agents, among others. For example, in someembodiments, a paramagnetic ion is one or more of chromium (III),manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper(II), neodymium (III), samarium (III), ytterbium (III), gadolinium(III), vanadium (II), terbium (III), dysprosium (III), holmium (III),erbium (III), lanthanum (III), gold (III), lead (II), and/or bismuth(III).

In some embodiments, a radioactive isotope is one or more ofastatine211, 14carbon, 51chromium, 36chlorine, 57cobalt, 58cobalt,copper67, 152Eu, gallium67, 3hydrogen, iodine123, iodine125, iodine131,indium 111, 59iron, 32phosphorus, radium223, rhenium186, rhenium 188,75selenium, 35sulphur, technicium99m, thorium227 and/or yttrium90.Radioactively labeled antibody agents may be produced according towell-known methods in the art. For instance, monoclonal antibodies canbe iodinated by contact with sodium and/or potassium iodide and achemical oxidizing agent such as sodium hypochlorite, or an enzymaticoxidizing agent, such as lactoperoxidase. Provided antibody agents maybe labeled with technetium99m by ligand exchange process, for example,by reducing pertechnate with stannous solution, chelating the reducedtechnetium onto a Sephadex column and applying the antibody to thiscolumn. In some embodiments, provided DV antibody agents are labeledusing direct labeling techniques, e.g., by incubating pertechnate, areducing agent such as SNC12, a buffer solution such as sodium-potassiumphthalate solution, and the antibody. Intermediary functional groupswhich are often used to bind radioisotopes which exist as metallic ionsto antibody are diethylenetriaminepentaacetic acid (DTPA) or ethylenediaminetetracetic acid (EDTA).

In some embodiments, a fluorescent label is or comprises one or more ofAlexa 350, Alexa 430, AMCA, BODIPY 630/650, BODIPY 650/665, BODIPY-FL,BODIPY-R6G, BODIPY-TMR, BODIPY-TRX, Cascade Blue, Cy3, Cy5,6-FAM,Fluorescein Isothiocyanate, HEX, 6-JOE, Oregon Green 488, Oregon Green500, Oregon Green 514, Pacific Blue, REG, Rhodamine Green, RhodamineRed, Renographin, ROX, TAMRA, TET, Tetramethylrhodamine, and/or TexasRed, among others.

Several methods are known in the art for the attachment or conjugationof an antibody agent to a payload. Some attachment methods involve theuse of a metal chelate complex employing, for example, an organicchelating agent such a diethylenetriaminepentaacetic acid anhydride(DTPA); ethylenetriaminetetraacetic acid; N-chloro-p-toluenesulfonamide;and/or tetrachloro-3α-6α-diphenylglycouril-3 attached to the antibody(U.S. Pat. Nos. 4,472,509 and 4,938,948, each incorporated herein byreference). Provided DV antibody agents may also be reacted with anenzyme in the presence of a coupling agent such as glutaraldehyde orperiodate. Conjugates with fluorescein markers are prepared in thepresence of these coupling agents or by reaction with an isothiocyanate.

Production of Antibodies

Provided antibody agents including antibodies, and/or characteristicportions thereof, or nucleic acids encoding them, may be produced by anyavailable means. Methods for generating antibodies (e.g., monoclonalantibodies and/or polyclonal antibodies) are well known in the art. Itwill be appreciated that a wide range of animal species can be used forthe production of antisera, including rabbit, mouse, rat, hamster,guinea pig or goat. The choice of animal may be decided upon the ease ofmanipulation, costs or the desired amount of sera, as would be known toone of skill in the art. It will be appreciated that antibody agent canalso be produced transgenically through the generation of a mammal orplant that is transgenic for the immunoglobulin heavy and light chainsequences of interest and production of the antibody in a recoverableform therefrom. In connection with the transgenic production in mammals,antibodies can be produced in, and recovered from, the milk of goats,cows, or other mammals. See, e.g., U.S. Pat. Nos. 5,827,690, 5,756,687,5,750,172, and 5,741,957.

Provided antibody agents (including antibodies and/or characteristicportions) may be produced, for example, by utilizing a host cell systemengineered to express an inventive antibody-encoding nucleic acid.Alternatively or additionally, provided antibody agents may be partiallyor fully prepared by chemical synthesis (e.g., using an automatedpeptide synthesizer).

Exemplary sources for antibody agent preparations suitable for theinvention include, but are not limited to, conditioned culture mediumderived from culturing a recombinant cell line that expresses a proteinof interest, or from a cell extract of, e.g., antibody-producing cells,bacteria, fungal cells, insect cells, transgenic plants or plant cells,transgenic animals or animal cells, or serum of animals, ascites fluid,hybridoma or myeloma supernatants. Suitable bacterial cells include, butare not limited to, Escherichia coli cells. Examples of suitable E. colistrains include: HB101, DH5α, GM2929, JM109, KW251, NM538, NM539, andany E. coli strain that fails to cleave foreign DNA. Suitable fungalhost cells that can be used include, but are not limited to,Saccharomyces cerevisiae, Pichiapastoris and Aspergillus cells. Suitableinsect cells include, but are not limited to, S2 Schneider cells, D.Mel-2 cells, SF9, SF21, High-5™, Mimic™-SF9, MG1 and KC1 cells. Suitableexemplary recombinant cell lines include, but are not limited to, BALB/cmouse myeloma line, human retinoblasts (PER.C6), monkey kidney cells,human embryonic kidney line (293), baby hamster kidney cells (BHK),Chinese hamster ovary cells (CHO), mouse sertoli cells, African greenmonkey kidney cells (VERO-76), human cervical carcinoma cells (HeLa),canine kidney cells, buffalo rat liver cells, human lung cells, humanliver cells, mouse mammary tumor cells, TRI cells, MRC 5 cells, FS4cells, and human hepatoma line (Hep G2).

Antibody agents of interest can be expressed using various vectors(e.g., viral vectors) known in the art and cells can be cultured undervarious conditions known in the art (e.g., fed-batch). Various methodsof genetically engineering cells to produce antibodies are well known inthe art. See e.g. Ausabel et al., eds. (1990), Current Protocols inMolecular Biology (Wiley, New York).

Provided antibody agents may be purified, if desired, using filtration,centrifugation and/or various chromatographic methods such as HPLC oraffinity chromatography. In some embodiments, fragments of providedantibody agents are obtained by methods which include digestion withenzymes, such as pepsin or papain, and/or by cleavage of disulfide bondsby chemical reduction.

Nucleic Acids

In certain embodiments, the present invention provides nucleic acidswhich encode an antibody agent. In some embodiments, the inventionprovides nucleic acids which are complementary to nucleic acids whichencode an antibody agent.

In some embodiments, the invention provides nucleic acid molecules whichhybridize to nucleic acids encoding an antibody agent. Such nucleicacids can be used, for example, as primers or as probes. To give but afew examples, such nucleic acids can be used as primers in polymerasechain reaction (PCR), as probes for hybridization (including in situhybridization), and/or as primers for reverse transcription-PCR(RT-PCR).

In certain embodiments, nucleic acids can be DNA or RNA, and can besingle stranded or double-stranded. In some embodiments, nucleic acidsmay include one or more non-natural nucleotides; In some embodiments,nucleic acids include only natural nucleotides.

Characterization and/or identification of DV-related agents

In some embodiments, the present invention provides antibody agents thatcan be used to identify and/or characterize one or more agents thatmimic an DV epitope or agent and/or induce a strong antibody response toDV.

In some embodiments, such agents include one or more antibody-likebinding peptidomimetics. Liu et al. Cell Mol Biol (Noisy-le-grand). 2003March; 49(2):209-16 describe “antibody like binding peptidomimetics”(ABiPs), which are peptides that act as pared-down antibodies and havecertain advantages of longer serum half-life as well as less cumbersomesynthesis methods. Likewise, in some aspects, antibody-like moleculesare cyclic or bicyclic peptides. For example, methods for isolatingantigen-binding bicyclic peptides (e.g., by phage display) and for usingthe such peptides are provided in U.S. Patent Pub. No. 20100317547,incorporated herein by reference.

In some embodiments, such agents include one or more antibody-likebinding scaffold proteins. For example, in some embodiments, one or moreCDRs arising from an antibody may be grafted onto a protein scaffold. Ingeneral, protein scaffolds may meet the greatest number of the followingcriteria: (Skerra A., J. Mol. Recogn., 2000, 13:167-187): goodphylogenetic conservation; known three-dimensional structure (as, forexample, by crystallography, NMR spectroscopy or any other techniqueknown to a person skilled in the art); small size; few or nopost-transcriptional modifications; and/or easy to produce, express andpurify. The origin of such protein scaffolds can be, but is not limitedto, fibronectin (e.g., fibronectin type III domain 10), lipocalin,anticalin (Skerra A., J. Biotechnol., 2001, 74(4):257-75), protein Zarising from domain B of protein A of Staphylococcus aureus, thioredoxinA or proteins with a repeated motif such as the “ankyrin repeat” (Kohlet al., PNAS, 2003, vol. 100, No. 4, 1700-1705), the “armadillo repeat”,the “leucine-rich repeat” and the “tetratricopeptide repeat”. Forexample, anticalins or lipocalin derivatives are described in US PatentPublication Nos. 20100285564, 20060058510, 20060088908, 20050106660, andPCT Publication No. WO2006/056464, incorporated herein by reference.Scaffolds derived from toxins such as, for example, toxins fromscorpions, insects, plants, mollusks, etc., and the protein inhibitorsof neuronal NO synthase (PIN) may also be used in accordance with thepresent invention.

In some embodiments, such agents include a mimotope, which can be usedto disrupt the interaction between an influenza virus and the HApolypeptide receptor. In some embodiment, the mimotope is used to elicitan antibody response identical or similar to the that elicited by itscorresponding target epitope. In some embodiments, the target epitope isa sequence that is conserved across more than one DV serotype. In someembodiment, the conserved epitope is a sequence that is conserved acrossDV serotypes 1-4. In some embodiments, the epitope is a conservedsequence located within the A-strand region of the E glycoprotein. Insome embodiments, a mimotope is a peptide. In some embodiments, amimotope is a small molecule, carbohydrate, lipid, or nucleic acid. Insome embodiments, mimotopes are peptide or non-peptide mimotopes ofconserved influenza epitopes. In some embodiments, by mimicking thestructure of a defined viral epitope, a mimotope interferes with theability of DV particles to bind to its natural binding partners, e.g.,by binding to the natural binding partner itself.

In some embodiments, such an agent is a stapled peptide. In someembodiments, the stapled peptide comprises an amino acid sequencesencoding one or more CDRs and/or FRs comprising at least greater than65, 70, 75, 80, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98or 99% homology and/or identity with the corresponding CDRs and/or FRsof an anti-DV antibody (e.g., 4E11). In some embodiments, the stapledpeptide comprises an amino acid sequence encoding one or more VH and/orVL chain sequence comprising at least greater than 65, 70, 75, 80, 85,86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% homologyand/or identity with the corresponding VH and VL chains of an anti-DVantibody (e.g., 4E11).

In certain embodiments, such an agent is or comprise a nucleic acid,such as DNA or RNA. In certain embodiments, nucleic acids can be DNA orRNA, and can be single stranded or double-stranded. In some embodiments,nucleic acids may include one or more non-natural nucleotides. In someembodiments, nucleic acids include only natural nucleotides. In someembodiments the nucleic acid is designed to mimic an epitope within a DVpolypeptide. In some embodiments the nucleic acid is designed to mimic aconserved epitope within one or more DV serotypes. In some embodiments,such an agent is or comprises one or more oligonucleotides. In someembodiments, such an agent is or comprises one or more oligonucleotidescomprising a secondary structure such as loop, hairpin, fold orcombinations thereof. In some embodiments, such an agent is or comprisesone or more oligonucleotides comprising a higher ordered (tertiary orquaternary) structure. In some embodiments, such an agent is orcomprises an aptamer.

In some embodiments, a vaccine may be designed to induce production ofantibodies that have been found to be lacking in the patient. In someembodiments, it is desirable for vaccine compositions to compriseantigens that have a native conformation, mediate a protective response(e.g., complement activation, virus neutralization, etc.), and/or caninduce a strong antibody response. In some embodiments, a vaccinecontains an epitope or mimotope thereof to which antibodies are notbeing produced naturally in the individual. For example, syntheticpeptide mimotopes isolated with DV antibodies (e.g., DV antibodiesrecognizing multiple serotypes) have the potential to induce a potentimmune response similar to the antibody used in the original isolationof the mimotope. Administration of such a vaccine might induce apatient's immune system to start producing a set of antibodies directedagainst the administered epitope. It will be appreciated that themimotopes (or epitopes) in accordance with the invention can be usedalone or in combination with recombinant proteins, inactivated DV virus,killed DV virus, and/or as a cocktail of several different mimotopes.

In some embodiments, vaccines to DV may be utilized for activeimmunization (i.e., immunization wherein microbes, proteins, peptides,epitopes, mimotopes, etc. are administered to a subject). In someembodiments, vaccines to DV may comprise any agent that mimics at leastone conformational epitope of DV A-strand region of DV envelopeglycoprotein may be used. For example, the agent may be a peptide,protein, glycopeptide, glycoprotein, small molecule, mimotope, organiccompound, lipid, saccharide, organometallic compound, inorganiccompound, etc. In some embodiments, epitopes represented in a vaccineinclude those against which antibodies known to prevent infection aredirected. In some embodiments, epitopes represented in a vaccine inaccordance with the invention include ones that are conserved amongdifferent genotypes and/or subtypes of the virus or among differentstrains of virus. In some embodiments, peptides or proteins that containconformationally defined epitopes of A-strand region of DV are used informulations of a vaccine to prevent, delay onset of, treat, amelioratesymptoms of, and/or reduce severity of infection by DV. In someembodiments, DV A-strand region epitopes may be linear epitopes. In someembodiments, A-strand region epitopes may be a mixture of linear andconformational epitopes. In some embodiments, A-strand region epitopesmay be conformational epitopes. In some embodiments, peptide epitopesare less than 100 amino acids in length. In certain embodiments, peptideepitopes are less than 50, less than 40, less than 30, less than 20, orless than 10 amino acids in length. In some embodiments, peptides to beused in formulating a vaccine are peptide fragments of A-strand regionprotein of DV. Typically, a peptide is used that folds in a mannersimilar to its three-dimensional fold in the native A-strand regionprotein, thus preserving the three-dimensional structure of theconformational epitope.

Systems for Identifying and/or Characterizing DV-binding agents

The present invention provides a variety of systems for testing,characterizing, and/or identifying DV antibody agents. In someembodiments, provided DV antibody agent are used to identify and/or tocharacterize other DV-binding agents (e.g., antibodies, polypeptides,small molecules, etc.).

In some embodiments, provided DV-binding agents are characterized bysuch systems and methods that involve contacting the DV-binding agentwith one or more candidate substrates, such as regions of DVpolypeptides, N-glycans on DV polypeptides, DV receptors, sialylated DVreceptors, and/or glycans on sialylated DV receptors.

In some embodiments, DV-binding agents (e.g., cross reactive antibodies)may be tested, characterized, and/or identified using computationalapproaches. In some embodiments, a computational approach involves usingphysicochemical features common to protein-protein (e.g.,antibody-antigen) interactions to predict protein-protein interactionand affinity enhancing mutations. Potency of antibodies, for example,produced using this approach in neutralizing DV could then be predictedby various assays known in the art (e.g., plaque reductionneutralization test, ELISA, hemagglutination assay, and Western blot).

In some embodiments, a DV-binding agent and/or candidate substrate maybe free in solution, fixed to a support, and/or expressed in and/or onthe surface of a cell. The candidate substrate and/or agents may belabeled, thereby permitting detection of binding. Either the DV-bindingagent or the candidate substrate is the labeled species. Competitivebinding formats may be performed in which one of the substances islabeled, and one may measure the amount of free label versus bound labelto determine the effect on binding.

In some embodiments, binding assays involve, for example, exposing acandidate substrate to a DV-binding agent and detecting binding betweenthe candidate substrate and the agent. A binding assay may be conductedin vitro (e.g., in a candidate tube, comprising substantially only thecomponents mentioned; in cell-free extracts; and/or in substantiallypurified components). Alternatively or additionally, binding assays maybe conducted in cyto and/or in vivo (e.g., within a cell, tissue, organ,and/or organism; described in further detail below).

In certain embodiments, at least one DV-binding agent is contacted withat least one candidate substrate and an effect detected. In someembodiments, for example, a DV-binding agent is contacted with acandidate substrate, and binding between the two entities is monitored.In some embodiments, an assay may involve contacting a candidatesubstrate with a characteristic portion of an agent. Binding of the DVagent to the candidate substrate is detected. It will be appreciatedthat fragments, portions, homologs, variants, and/or derivatives ofDV-binding agents may be employed, provided that they comprise theability to bind one or more candidate substrates.

Binding of a DV agent to the candidate substrate may be determined by avariety of methods well-known in the art. In some embodiments, bindingmeasurements may be conducted using SPR analysis. In some embodiments,SPR analysis may be used to measure affinity and kinetic bindingparameters of a DV-binding agent. In some embodiments, assays involvingsolid phase-bound DV agents and detecting their interactions with one ormore candidate substrates may be used. Thus, a DV-binding agent maycomprise a detectable marker, such as a radioactive, fluorescent, and/orluminescent label. Furthermore, candidate substrate can be coupled tosubstances which permit indirect detection (e.g. by means of employingan enzyme which uses a chromogenic substrate and/or by means of bindinga detectable antibody). Changes in the conformation of DV-binding agentsas the result of an interaction with a candidate substrate may bedetected, for example, by the change in the emission of the detectablemarker. Alternatively or additionally, solid phase-bound proteincomplexes may be analyzed by means of mass spectrometry.

In some embodiments, the DV-binding agent can be non-immobilized. Insome embodiments, the non-immobilized component may be labeled (with forexample, a radioactive label, an epitope tag, an enzyme-antibodyconjugate, etc.). Alternatively or additionally, binding may bedetermined by immunological detection techniques. For example, thereaction mixture may be subjected to Western blotting and the blotprobed with an antibody that detects the non-immobilized component.Alternatively or additionally, ELISA may be utilized to assay forbinding. In some embodiments, binding affinity of a DV agent to acandidate substrate may be determined by using a high throughputindirect ELISA assay.

In some embodiments, focus reduction neutralization test (FRNT) assaymay be utilized for measuring activity or neutralizing potency of aDV-binding agent. In some embodiments, animal host may be used formeasuring anti-DV activity in vivo.

In certain embodiments, cells may be directly assayed for bindingbetween DV agents and candidate substrates. Immunohistochemicaltechniques, confocal techniques, and/or other techniques to assessbinding are well known to those of skill in the art. Various cell linesmay be utilized for such screening assays, including cells specificallyengineered for this purpose. Examples of cells used in the screeningassays include mammalian cells, fungal cells, bacterial cells, or viralcells. A cell may be a stimulated cell, such as a cell stimulated with agrowth factor. One of skill in the art would understand that theinvention disclosed herein contemplates a wide variety of in cyto assaysfor measuring the ability of DV-binding agents to bind to candidatesubstrates.

Depending on the assay, cell and/or tissue culture may be required. Acell may be examined using any of a number of different physiologicassays. Alternatively or additionally, molecular analysis may beperformed, including, but not limited to, western blotting to monitorprotein expression and/or test for protein-protein interactions; massspectrometry to monitor other chemical modifications; etc.

In some embodiments, a binding assays described herein may be performedusing a range of concentrations of DV-binding agents and/or candidatesubstrates. In some embodiments, the binding assays described herein areused to assess the ability of a candidate substrate to bind to a DVagent over range of antibody concentrations (e.g. greater than about 100μg/ml, about 100 μg/ml, about 50 μg/ml, about 40 μg/ml, about 30 μg/ml,about 20 μg/ml, about 10 μg/ml, about 5 μg/ml, about 4 μg/ml, about 3μg/ml, about 2 μg/ml, about 1.75 μg/ml, about 1.5 μg/ml, about 1.25μg/ml, about 1.0 μg/ml, about 0.9 μg/ml, about 0.8 μg/ml, about 0.7μg/ml, about 0.6 μg/ml, about 0.5 μg/ml, about 0.4 μg/ml, about 0.3μg/ml, about 0.2 μg/ml, about 0.1 μg/ml, about 0.05 μg/ml, about 0.01μg/ml, and/or less than about 0.01 μg/ml).

In some embodiments, any of the binding studies described herein can beexecuted in a high throughput fashion. Using high throughput assays, itis possible to screen up to several thousand agents in a single day. Insome embodiments, each well of a microtiter plate can be used to run aseparate assay against a selected candidate substrate, or, ifconcentration and/or incubation time effects are to be observed, every5-10 wells can test a single candidate substrate. Thus, a singlestandard microtiter plate can assay up to 96 binding interactionsbetween agents and candidate substrates; if 1536 well plates are used,then a single plate can assay up to 1536 binding interactions betweenagents and candidate substrates; and so forth. It is possible to assaymany plates per day. For example, up to about 6,000, about 20,000, about50,000, or more than about 100,000 assay screens can be performed onbinding interactions between antibodies and candidate substrates usinghigh throughput systems in accordance with the present invention.

In some embodiments, such methods utilize an animal host. As usedherein, an “animal host” includes any animal model suitable forinfluenza research. For example, animal hosts suitable for the inventioncan be any mammalian hosts, including primates, ferrets, cats, dogs,cows, horses, rodents such as, mice, hamsters, rabbits, and rats. Incertain embodiments, an animal host used for the invention is a ferret.In particular, in some embodiments, an animal host is naïve to viralexposure or infection prior to administration of an agent (optionally inan inventive composition). In some embodiments, the animal host isinoculated with, infected with, or otherwise exposed to virus prior toor concurrent with administration of an agent. An animal host used inthe practice of the present invention can be inoculated with, infectedwith, or otherwise exposed to virus by any method known in the art. Insome embodiments, an animal host may be inoculated with, infected with,or exposed to virus intranasally.

Naïve and/or inoculated animals may be used for any of a variety ofstudies. For example, such animal models may be used for virustransmission studies as in known in the art. It is contemplated that theuse of ferrets in virus transmission studies may serve as a reliablepredictor for virus transmission in humans. Virus transmission studiesmay be used to test agents. For example, DV-binding agents may beadministered to a suitable animal host before, during or after virustransmission studies in order to determine the efficacy of said agent inblocking virus binding and/or infectivity in the animal host. Usinginformation gathered from virus transmission studies in an animal host,one may predict the efficacy of an agent in blocking virus bindingand/or infectivity in a human host.

Pharmaceutical Compositions

The present invention provides compositions comprising one or moreprovided antibody agents. In some embodiments the present inventionprovides at least one antibody and at least one pharmaceuticallyacceptable excipient. Such pharmaceutical compositions may optionallycomprise and/or be administered in combination with one or moreadditional therapeutically active substances. In some embodiments,provided pharmaceutical compositions are useful in medicine. In someembodiments, provided pharmaceutical compositions are useful asprophylactic agents (i.e., vaccines) in the treatment or prevention ofDV infection or of negative ramifications associated or correlated withDV infection. In some embodiments, provided pharmaceutical compositionsare useful in therapeutic applications, for example in individualssuffering from or susceptible to DV infection. In some embodiments,pharmaceutical compositions are formulated for administration to humans.

For example, pharmaceutical compositions provided herein may be providedin a sterile injectible form (e.g., a form that is suitable forsubcutaneous injection or intravenous infusion). For example, in someembodiments, pharmaceutical compositions are provided in a liquid dosageform that is suitable for injection. In some embodiments, pharmaceuticalcompositions are provided as powders (e.g. lyophilized and/orsterilized), optionally under vacuum, which are reconstituted with anaqueous diluent (e.g., water, buffer, salt solution, etc.) prior toinjection. In some embodiments, pharmaceutical compositions are dilutedand/or reconstituted in water, sodium chloride solution, sodium acetatesolution, benzyl alcohol solution, phosphate buffered saline, etc. Insome embodiments, powder should be mixed gently with the aqueous diluent(e.g., not shaken).

In some embodiments, provided pharmaceutical compositions comprise oneor more pharmaceutically acceptable excipients (e.g., preservative,inert diluent, dispersing agent, surface active agent and/or emulsifier,buffering agent, etc.). In some embodiments, pharmaceutical compositionscomprise one or more preservatives. In some embodiments, pharmaceuticalcompositions comprise no preservative.

In some embodiments, pharmaceutical compositions are provided in a formthat can be refrigerated and/or frozen. In some embodiments,pharmaceutical compositions are provided in a form that cannot berefrigerated and/or frozen. In some embodiments, reconstituted solutionsand/or liquid dosage forms may be stored for a certain period of timeafter reconstitution (e.g., 2 hours, 12 hours, 24 hours, 2 days, 5 days,7 days, 10 days, 2 weeks, a month, two months, or longer).

Liquid dosage forms and/or reconstituted solutions may compriseparticulate matter and/or discoloration prior to administration. In someembodiments, a solution should not be used if discolored or cloudyand/or if particulate matter remains after filtration.

Formulations of the pharmaceutical compositions described herein may beprepared by any method known or hereafter developed in the art ofpharmacology. In some embodiments, such preparatory methods include thestep of bringing active ingredient into association with one or moreexcipients and/or one or more other accessory ingredients, and then, ifnecessary and/or desirable, shaping and/or packaging the product into adesired single- or multi-dose unit.

A pharmaceutical composition in accordance with the invention may beprepared, packaged, and/or sold in bulk, as a single unit dose, and/oras a plurality of single unit doses. As used herein, a “unit dose” isdiscrete amount of the pharmaceutical composition comprising apredetermined amount of the active ingredient. The amount of the activeingredient is generally equal to a dose which would be administered to asubject and/or a convenient fraction of such a dose such as, forexample, one-half or one-third of such a dose.

Relative amounts of active ingredient, pharmaceutically acceptableexcipient, and/or any additional ingredients in a pharmaceuticalcomposition in accordance with the invention may vary, depending uponthe identity, size, and/or condition of the subject treated and/ordepending upon the route by which the composition is to be administered.By way of example, the composition may comprise between 0.1% and 100%(w/w) active ingredient.

Pharmaceutical compositions of the present invention may additionallycomprise a pharmaceutically acceptable excipient, which, as used herein,may be or comprise solvents, dispersion media, diluents, or other liquidvehicles, dispersion or suspension aids, surface active agents, isotonicagents, thickening or emulsifying agents, preservatives, solid binders,lubricants and the like, as suited to the particular dosage formdesired. Remington's The Science and Practice of Pharmacy, 21st Edition,A. R. Gennaro, (Lippincott, Williams & Wilkins, Baltimore, Md., 2006)discloses various excipients used in formulating pharmaceuticalcompositions and known techniques for the preparation thereof. Exceptinsofar as any conventional excipient medium is incompatible with asubstance or its derivatives, such as by producing any undesirablebiological effect or otherwise interacting in a deleterious manner withany other component(s) of the pharmaceutical composition, its use iscontemplated to be within the scope of this invention.

Vaccines

In some embodiments, the present invention provides vaccine compositionsfor use, and/or for exam in passive immunization (i.e., immunizationwherein antibodies are administered to a subject) of a subject who issuffering from or susceptible to DV infection. In some embodiments,passive immunization occurs when antibodies are transferred from motherto fetus during pregnancy. In some embodiments, passive immunizationincludes administration of antibody agents directly to an individual(e.g., by injection, orally, nasally, etc.).

In some embodiments, prophylactic applications may include administeringvaccines. In some embodiments, vaccination is tailored to the individualpatient. For example, as described below, serum may be collected from apatient and tested for presence of DV, and in some embodiments for oneor more particular DV serotypes. In some embodiments, appropriaterecipients of provided vaccines are individuals suffering from orsusceptible to infection with one or more DV serotypes bound and/orneutralized by a provided antibody.

In some embodiments, a vaccine is administered orally, intranasally,subcutaneously, intramuscularly, intradermally, or via any othermedically-appropriate route of administration. It will be appreciatedthat each route of administration may require distinct formulations ordelivery mechanisms and such variable parameters are contemplated aswithin the scope of the present invention. In some embodiments, theroute of administration and/or formulation may be dictated in part bythe age and/or condition of the subject. For example, administration ofa vaccine to a baby may be performed via injection to the anterolateralaspect of the thigh, due to the large muscle mass. In some embodiments,where the subject is a child or an adult, administration of a vaccine tothe deltoid muscle may be preferred. It is understood that soundsmedical judgment should be used to determine the proper route and/orformulation for administration to a particular subject.

In some embodiments, a vaccine composition comprises at least oneadjuvant. Any adjuvant may be used in accordance with the presentinvention. A large number of adjuvants are known; a useful compendium ofmany such compounds is prepared by the National Institutes of Health andcan be found on www.niaid.nih.gov/daids/vaccine/pdf/compendium.pdf; seealso Allison (1998, Dev. Biol. Stand., 92:3-11; incorporated herein byreference), Unkeless et al. (1998, Annu. Rev. Immunol., 6:251-281;incorporated herein by reference), and Phillips et al. (1992, Vaccine,10:151-158; incorporated herein by reference). Hundreds of differentadjuvants are known in the art and could be employed in the practice ofthe present invention. Exemplary adjuvants that can be utilized inaccordance with the invention include, but are not limited to,cytokines, gel-type adjuvants (e.g., aluminum hydroxide, aluminumphosphate, calcium phosphate, etc.); microbial adjuvants (e.g.,immunomodulatory DNA sequences that include CpG motifs; endotoxins suchas monophosphoryl lipid A; exotoxins such as cholera toxin, E. coli heatlabile toxin, and pertussis toxin; muramyl dipeptide, etc.);oil-emulsion and emulsifier-based adjuvants (e.g., Freund's Adjuvant,MF59 [Novartis], SAF, etc.); particulate adjuvants (e.g., liposomes,biodegradable microspheres, saponins, etc.); synthetic adjuvants (e.g.,nonionic block copolymers, muramyl peptide analogues, polyphosphazene,synthetic polynucleotides, etc.); and/or combinations thereof. Otherexemplary adjuvants include some polymers (e.g., polyphosphazenes;described in U.S. Pat. No. 5,500,161, which is incorporated herein byreference), Q57, QS21, squalene, tetrachlorodecaoxide, etc.Pharmaceutically acceptable excipients have been previously described infurther detail in the above section entitled “PharmaceuticalCompositions.”

Combination Therapy

It will be appreciated that DV antibody agents in accordance with thepresent invention and/or pharmaceutical compositions thereof can beemployed in combination therapies. By “in combination with,” it is notintended to imply that the agents must be administered at the same timeand/or formulated for delivery together, although these methods ofdelivery are within the scope of the invention. Compositions can beadministered concurrently with, prior to, or subsequent to, one or moreother desired therapeutics or medical procedures. In will be appreciatedthat therapeutically active agents utilized in combination may beadministered together in a single composition or administered separatelyin different compositions. In general, each agent will be administeredat a dose and/or on a time schedule determined for that agent.

The particular combination of therapies (e.g., therapeutics orprocedures) to employ in a combination regimen will take into accountcompatibility of the desired therapeutics and/or procedures and thedesired therapeutic effect to be achieved. It will also be appreciatedthat pharmaceutical compositions of the present invention can beemployed in combination therapies (e.g., combination vaccine therapies),that is, the pharmaceutical compositions can be administeredconcurrently with, prior to, or subsequent to, one or more other desiredtherapeutic and/or vaccination procedures.

Therapeutically effective amounts of antibody agents in accordance withthe invention combined with for use in combination with a providedpharmaceutical composition and at least one other active ingredient. Insome embodiments, an active ingredient is an anti-viral agent, such as,but not limited to, interferons (e.g., interferon α-2b, interferon-γ,etc.), anti-DV monoclonal antibodies, anti-DV polyclonal antibodies, RNApolymerase inhibitors, protease inhibitors, helicase inhibitors,immunomodulators, antisense compounds, short interfering RNAs, shorthairpin RNAs, micro RNAs, RNA aptamers, ribozymes, and combinationsthereof. The particular combination of therapies to employ in acombination regimen will generally take into account compatibility ofthe desired therapeutics and/or procedures and the desired therapeuticeffect to be achieved. It will also be appreciated that the therapiesand/or vaccines employed may achieve a desired effect for the samedisorder (for example, an inventive antigen may be administeredconcurrently with another DV vaccine), or they may achieve differenteffects.

It will be appreciated that the therapies employed may achieve a desiredeffect for the same purpose (for example, DV antibodies useful fortreating, preventing, and/or delaying the onset of DV infection may beadministered concurrently with another agent useful for treating,preventing, and/or delaying the onset of DV infection), or they mayachieve different effects (e.g., control of any adverse effects). Theinvention encompasses the delivery of pharmaceutical compositions incombination with agents that may improve their bioavailability, reduceand/or modify their metabolism, inhibit their excretion, and/or modifytheir distribution within the body.

In some embodiments, agents utilized in combination with be utilized atlevels that do not exceed the levels at which they are utilizedindividually. In some embodiments, the levels utilized in combinationwill be lower than those utilized individually.

In some embodiments, DV antibodies in accordance with the invention maybe administered with interferon, with RNA polymerase inhibitors, or withboth interferon and RNA polymerase inhibitors.

In some embodiments, combination therapy may involve administrations ofa plurality of antibody agents directed to a single epitope (e.g. asingle conformational epitope). In some embodiments, combination therapycan comprise a plurality of antibody agents that recognize distinctepitopes (e.g., on the same viral envelope protein or on different viralenvelope proteins, where epitopes may or may not be conformational), forexample to simultaneously interfere with multiple mechanisms in theinfectious process.

In certain embodiments, compositions in accordance with the inventioncomprise exactly one antibody agent to A-strand region. In certainembodiments, compositions include and/or combination therapy utilizeexactly two DV A-strand region antibody agents.

It will be appreciated by one of skill in the art that any permutationor combination of antibody agents in accordance with the presentinvention can be combined with any other antibody agent to formulatecompositions and/or combination therapy regimens comprising a pluralityof different antibody agents.

Methods of Administration

DV antibody agents in accordance with the invention and pharmaceuticalcompositions thereof in accordance with the present invention may beadministered according to any appropriate route and regimen. In someembodiments, a route or regimen is one that has been correlated with apositive therapeutic benefit. In some embodiments, a route or regimen isone that has been approved by the FDA and/or EP.

In some embodiments, the exact amount administered may vary from subjectto subject, depending on one or more factors as is well known in themedical arts. Such factors may include, for example, one or more ofspecies, age, general condition of the subject, severity of theinfection, particular composition, its mode of administration, its modeof activity, the disorder being treated and the severity of thedisorder; the activity of the specific DV antibody agent employed; thespecific pharmaceutical composition administered; the half-life of thecomposition after administration; the age, body weight, general health,sex, and diet of the subject; the time of administration, route ofadministration, and rate of excretion of the specific compound employed;the duration of the treatment; drugs used in combination or coincidentalwith the specific compound employed and the like. Pharmaceuticalcompositions may be formulated in dosage unit form for ease ofadministration and uniformity of dosage. It will be understood, however,that the total daily usage of the compositions of the present inventionwill be decided by the attending physician within the scope of soundmedical judgment.

Pharmaceutical compositions of the present invention may be administeredby any route, as will be appreciated by those skilled in the art. Insome embodiments, pharmaceutical compositions of the present inventionare administered by oral (PO), intravenous (IV), intramuscular (IM),intra-arterial, intramedullary, intrathecal, subcutaneous (SQ),intraventricular, transdermal, interdermal, intradermal, rectal (PR),vaginal, intraperitoneal (IP), intragastric (IG), topical (e.g., bypowders, ointments, creams, gels, lotions, and/or drops), mucosal,intranasal, buccal, enteral, vitreal, sublingual; by intratrachealinstillation, bronchial instillation, and/or inhalation; as an oralspray, nasal spray, and/or aerosol, and/or through a portal veincatheter.

In specific embodiments, DV antibody agents in accordance with thepresent invention and/or pharmaceutical compositions thereof may beadministered intravenously, for example, by intravenous infusion. Inspecific embodiments, DV antibody agents in accordance with the presentinvention and/or pharmaceutical compositions thereof may be administeredby intramuscular injection. In specific embodiments, DV antibody agentsin accordance with the present invention and/or pharmaceuticalcompositions thereof may be administered by subcutaneous injection. Inspecific embodiments, DV antibody agents in accordance with the presentinvention and/or pharmaceutical compositions thereof may be administeredvia portal vein catheter. However, the invention encompasses thedelivery of DV antibody agents in accordance with the present inventionand/or pharmaceutical compositions thereof by any appropriate routetaking into consideration likely advances in the sciences of drugdelivery.

In certain embodiments, DV antibody agents in accordance with thepresent invention and/or pharmaceutical compositions thereof inaccordance with the invention may be administered at dosage levelssufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, fromabout 0.01 mg/kg to about 50 mg/kg, from about 0.1 mg/kg to about 40mg/kg, from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg toabout 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, or from about 1mg/kg to about 25 mg/kg of subject body weight per day to obtain thedesired therapeutic effect. The desired dosage may be delivered morethan three times per day, three times per day, two times per day, onceper day, every other day, every third day, every week, every two weeks,every three weeks, every four weeks, every two months, every six months,or every twelve months. In certain embodiments, the desired dosage maybe delivered using multiple administrations (e.g., two, three, four,five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen,or more administrations).

Prophylactic Applications

In some embodiments, DV antibody agents in accordance with the inventionmay be utilized for prophylactic applications. In some embodiments,prophylactic applications involve systems and methods for preventing,inhibiting progression of, and/or delaying the onset of DV infection,and/or any other DV-associated condition in individuals susceptible toand/or displaying symptoms of DV infection. In some embodiments,prophylactic applications involve systems and methods for preventing,inhibiting progression of, and/or delaying the onset of infection of thebrain. In some embodiments, prophylactic applications involve systemsand methods for preventing, inhibiting progression of, and/or delayingthe impairment of vital organs (e.g., liver).

Diagnostic Applications

In some embodiments, DV antibody agents in accordance with the inventionare used for diagnostic applications. For example, by virtue of thevariety of binding profiles of DV antibody agents, diagnostic assays maybe employed which will detect a plurality of DV serotypes, so as toprovide a pan-DV antibody agent, while at the same time being able todissect individual serotypes by subtractive analysis.

For diagnostic purposes, antibody agents may be used in a wide varietyof formats for detecting A-strand region of envelope glycoprotein,discerning DV serotypes, detecting virions and antibodies (see, e.g.,U.S. Pat. No. 5,695,390; incorporated herein by reference). Antibodyagents may be used individually or in combination with other antibodiesof the subject group or other antibodies or with lectins which bind tothe glycosyl groups present on DV envelope proteins. For diagnosticpurposes, a wide variety of labels may be employed, which for the mostpart have been mentioned previously. These include, but are not limitedto, fluorophores, chemiluminescent moieties, radioisotopes, enzymes,particles (e.g., colloidal carbon particles, gold particles, latexparticles, etc.) ligands for which there are high affinity receptors,and prolabels, which can be activated to provide a detectable signal.

In some embodiments, a surface is coated with a protein, which can bindto DV antigens as free protein (e.g., circulating proteins) or as partof an intact or partially intact virion. One may use antibodies of thesubject invention which bind to multiple DV serotypes or to lectins(e.g., Galanthus nivalis lectin; “GNA”).

In some embodiments, assays may involve contacting a surface with amedium, which may contain free or DV-associated protein(s), where themedium may be the sample or a solution of known A-strand region of oneor more serotypes. After incubation and washing to removenon-specifically bound protein, the assay may proceed in various mannersdepending upon what is being assayed. Where a blood sample suspected ofbeing seropositive is being assayed, the sample may be applied to thelayer of A-strand region protein, incubated, and washed, and thepresence of human antibodies bound to the protein layer determined. Onemay use labeled t-human antibodies (other than against the isotype ofthe subject antibodies, where the subject antibodies have been initiallyused). In assays for antibodies in seropositive subjects, subjectantibodies may be used as controls with the same reagent used to detectany human anti-DV antibodies in the sera of such subjects. Thespecificity of the antibodies in the sample can be confirmed by usingthe subject antibodies, which are differentially labeled from theanti-human antibodies and determine whether they are blocked by theantibodies in the sample.

Where the sample is assayed for DV A-strand region protein, detectionemploys labeled subject antibodies, the selection depending upon whetherone is interested in genotyping or detection of A-strand region protein.After washing away non-specifically bound antibody, the presence oflabeled antibodies is determined by detecting the presence of the labelin accordance with known techniques. Alternatively or additionally,where the subject antibodies are bound to a surface, a labeled lectinfor A-strand region may be employed to detect the presence of A-strandregion protein.

Antibody agents in accordance with the invention can be used to measurethe reactivity of other antibodies, including antibodies in sera,monoclonal antibodies, antibodies expressed as a result of geneticengineering, etc. In some embodiments, intact virions are used. In someembodiments, conformationally conserved envelope proteins are used. Forvirion capture, see, for example, Kimura et al., 1998, J. Med. Virology,56:25-32; Morita et al., 1996, Hapato-Gastroenterology, 43:582-585; Sataet al., 1993, Virology, 196:354-357; and Hijikata et al., 1993, J.Virol., 67:1953-1958; all of which are incorporated herein by reference.One protocol involves steps of coating a solid support with a lectin(e.g., GNA) and then contacting the surface with a medium (e.g., serumof a seropositive patient) comprising intact DV virions. Additives whichmight destroy virions should usually be avoided (e.g., detergents).After incubating the medium and washing to remove non-specifically boundcomponents of the medium, virions may be contacted with antibodies inaccordance with the invention and antibodies of the sample. This may beperformed concurrently or consecutively, where the sample is addedfirst. An amount of the subject antibody is used which is sensitive todisplacement by another antibody. Such amount may be determinedempirically, and one may wish to use different amounts of the subjectantibody in a series of tests. By knowing the signal, which is obtainedin the absence and presence of the sample, one can determine thereactivity or binding affinity of the antibodies in the sample. Varioustechniques may be used to determine the amount of a subject antibodybound to the virions. Where the subject antibodies are labeled, e.g.,with biotin or digoxigenin, streptavidin or anti-digoxigenin labeledwith a fluorophore or enzyme whose substrate produces a detectablesignal can serve to determine the amount of the subject antibodies.

Labeled subject antibody agents may be used in assaying for the presenceof DV from biopsy material. Labeled antibody may be incubated withimmobilized biopsy material, such as a liver slice, with a solution ofone or more of the subject labeled antibodies. After washing awaynon-specifically bound antibodies, the presence of the antibodies boundto the cells of the biopsied tissue may be detected in accordance withthe nature of the label.

In some embodiments, DV antibody agents in accordance with the inventioncan be used to identify DV receptors. Those skilled in the art willappreciate the multitude of ways this can be accomplished (Sambrook J.,Fritsch E. and Maniatis T. Molecular Cloning: A Laboratory Manual. ColdSpring Harbor Press, Cold Spring Harbor, N.Y., 1989; and Ausubel et al.,eds., Current Protocols in Molecular Biology, 1987; both of which areincorporated herein by reference). Typically, protein and peptidereceptors can be identified by determining whether an antibody toA-strand region of DV envelope glycoprotein can inhibit attachment of DVvirions to a cell susceptible to DV infection. Thus, receptors for DVA-strand region proteins and peptides can be identified in this manner.A susceptible cell can be incubated in the presence of DV and anti-DVA-strand region antibody, and a cell-binding assay can be utilized todetermine whether attachment is decreased in the presence of theantibody.

Cells expressing putative receptors for DV and/or libraries of putativereceptors for DV may be screened for their abilities to bind DV. Forexample, cells expressing a putative DV receptor (e.g., a receptor forDV A-strand region) can be contacted with an DV protein or peptide inthe presence of an antibody for a time and under conditions sufficientto allow binding of the DV protein or peptide to putative receptor onthe surface of the cell. Alternatively or additionally, DV proteins,peptides, or virions can be pre-incubated with antibody prior tocontacting the putative receptor on the cell surface. Binding can bedetected by any means known in the art, e.g., flow cytometry etc. (seeAusubel et al. or Sambrook et al., supra). A decrease in binding to thesurface of the cell in the presence of antibody compared to binding inthe absence of the cell in the absence of the antibody indicates theidentification of an DV receptor.

In some embodiments, methods of identifying DV receptors include the useof solid supports, such as beads, columns, and the like. For example,receptors for DV proteins and peptides (e.g., A-strand region proteinsand/or fragments thereof) and/or DV virions can be identified byattaching an DV antibody to a solid support and then contacting theantibody with an DV protein or peptide for a time sufficient for the DVprotein or peptide to bind to the antibody. This provides an DV proteinligand for putative DV receptors that can be contacted with theantibody:ligand complex on the solid support for a time and underconditions sufficient to allow binding of a receptor to the DV proteinor peptide. Proteins can be expressed from a library or provided as acell extract or purified protein preparation from natural or recombinantcells. Once specific binding complexes between the DV protein peptideare formed, unbound DV proteins or peptides, e.g., library proteins orpeptide that did not bind specifically to the DV proteins or peptides,are removed, e.g., by standard washing steps. Bound proteins are theneluted and identified, e.g., by gel electrophoresis.

Kits

The invention provides a variety of kits for conveniently and/oreffectively carrying out methods in accordance with the presentinvention. Kits typically comprise one or more DV antibody agents inaccordance with the invention. In some embodiments, kits comprise acollection of different DV antibody agents to be used for differentpurposes (e.g., diagnostics, treatment, and/or prophylaxis). Typicallykits will comprise sufficient amounts of DV antibody agents to allow auser to perform multiple administrations to a subject(s) and/or toperform multiple experiments. In some embodiments, kits are suppliedwith or include one or more DV antibody agents that have been specifiedby the purchaser.

In certain embodiments, kits for use in accordance with the presentinvention may include one or more reference samples; instructions (e.g.,for processing samples, for performing tests, for interpreting results,for solubilizing DV antibody agents, for storage of DV antibody agents,etc.); buffers; and/or other reagents necessary for performing tests. Incertain embodiments kits can comprise panels of antibodies. Othercomponents of kits may include cells, cell culture media, tissue, and/ortissue culture media.

Kits may comprise instructions for use. For example, instructions mayinform the user of the proper procedure by which to prepare apharmaceutical composition comprising DV antibody agents and/or theproper procedure for administering pharmaceutical compositions to asubject.

In some embodiments, kits include a number of unit dosages of apharmaceutical composition comprising DV antibody agents. A memory aidmay be provided, for example in the form of numbers, letters, and/orother markings and/or with a calendar insert, designating the days/timesin the treatment schedule in which dosages can be administered. Placebodosages, and/or calcium dietary supplements, either in a form similar toor distinct from the dosages of the pharmaceutical compositions, may beincluded to provide a kit in which a dosage is taken every day.

Kits may comprise one or more vessels or containers so that certain ofthe individual components or reagents may be separately housed. Kits maycomprise a means for enclosing the individual containers in relativelyclose confinement for commercial sale, e.g., a plastic box, in whichinstructions, packaging materials such as styrofoam, etc., may beenclosed.

In some embodiments, kits are used in the treatment, diagnosis, and/orprophylaxis of a subject suffering from and/or susceptible to DV. Insome embodiments, such kits comprise (i) at least one DV antibody agent;(ii) a syringe, needle, applicator, etc. for administration of the atleast one DV antibody agent to a subject; and (iii) instructions foruse.

In some embodiments, kits are used in the treatment, diagnosis, and/orprophylaxis of a subject suffering from and/or susceptible to DV. Insome embodiments, such kits comprise (i) at least one DV antibody agentprovided as a lyophilized powder; and (ii) a diluent for reconstitutingthe lyophilized powder. Such kits may optionally comprise a syringe,needle, applicator, etc. for administration of the at least one DVantibody agent to a subject; and/or instructions for use.

The present invention provides kits containing reagents for thegeneration of vaccines comprising at least one DV antibody agent. Insome embodiments, such kits may include cells expressing DV antibodies,characteristic portions thereof, and/or biologically active portionsthereof; (ii) media for growing the cells; and (iii) columns, resin,buffers, tubes, and other tools useful for antibody purification. Insome embodiments, such kits may include (i) plasmids containingnucleotides encoding DV antibodies, characteristic portions thereof,and/or biologically active portions thereof; (ii) cells capable of beingtransformed with the plasmids, such as mammalian cell lines, includingbut not limited to, Vero and MDCK cell lines; (iii) media for growingthe cells; (iv) expression plasmids containing no nucleotides encodingDV antibodies as negative controls; (v) columns, resin, buffers, tubes,and other tools useful for antibody purification; and (vi) instructionsfor use.

In some embodiments, kits are used to detect the presence of DV in oneor more samples. Such samples may be pathological samples, including,but not limited to, blood, serum/plasma, peripheral blood mononuclearcells/peripheral blood lymphocytes (PBMC/PBL), sputum, urine, feces,throat swabs, dermal lesion swabs, cerebrospinal fluids, cervicalsmears, pus samples, food matrices, and tissues from various parts ofthe body such as brain, spleen, and liver. Such samples may beenvironmental samples, including, but not limited to, soil, water, andflora. Other samples that have not been listed may also be applicable.In some embodiments, such kits comprise (i) at least one DV antibody;(ii) a sample known to contain DV, as a positive control; and (iii) asample known not to contain DV, as a negative control; and (iv)instructions for use.

In some embodiments, kits are used to neutralize DV in one or moresamples. Such kits may provide materials needed to treat anDV-containing sample with at least one DV antibody agent and to test theability of the treated sample to infect cultured cells relative tountreated sample. Such kits may include (i) at least one DV antibodyagent; (ii) cells capable of being cultured and infected with DV; (iii)an antibody that is incapable of binding to and neutralizing DV, as anegative control; (iv) an antibody that is capable of binding to andneutralizing DV, as a positive control; (v) a sample known not tocontain DV, as a negative control; (vi) a sample known to contain DV, asa positive control; and (vii) instructions for use.

EXAMPLES

The present invention will be better understood in connection with thefollowing Examples. However, it should be understood that these examplesare for illustrative purposes only and are not meant to limit the scopeof the invention. Various changes and modifications to the disclosedembodiments will be apparent to those skilled in the art and suchchanges and modifications including, without limitation, those relatingto the formulations and/or methods of the invention may be made withoutdeparting from the spirit of the invention and the scope of the appendedclaims.

Example 1: Prediction of Protein-Protein Complex Structure by AnalyzingPhysicochemical Features of the Interaction

Studies in this Example illustrate the development and use of keyphysicochemical features to model a protein-protein (e.g.,antigen-antibody) interaction. Analysis in this Example assists indistinguishing accurate native-like structures for an antigen-antibodyinteraction from inaccurate structures and thus, helps in overcoming thelimitations of using only energetic functions to rank poses, asperformed in modeling of protein-protein interaction using computationaldocking models. Furthermore, the failure to identify the native pose ofnine test cases analyzed in this Example, highlights the limitations ofthe current search algorithm and the challenges associated withdesigning affinity enhancing mutations for antigen-antibody complexes.

To capture as many geometrical and chemical properties that form thebasis of a molecular recognition, thirteen atomic level features: sevenchemical and six physical (Table 1) were used to describe anantigen-antibody interface. Further, a data set comprising of 77non-redundant 3D structures of antigen-antibody complexes was assembled(see Methods section) and split into two parts, a training setconsisting of 40 structures and a test set consisting of the remaining37 structures. Corresponding to each structure, 100 decoy models wereconstructed using computational docking (see Methods section), yieldinga total of 7,777 structures (7,700 decoy+77 x-ray). In the trainingphase, multivariate logistic regression analysis (MLR) was used todetermine the relationship between each feature (explanatory variable)and the degree to which it can successfully discriminate x-ray versusdecoys poses (outcome variable). This analysis assisted in achieving asubset of all the explanatory variables that could be combined topredict the value of the outcome variable. Input features generated fromeach PDB file (and its decoys) were represented as standardized Z-scoresto prevent non-uniform learning, which can lead to over (or under)estimation of significance. For the prediction phase, the pre-computedsignificant features were employed to predict the probability that astructure in the test data set is native-like.

The results from MLR analysis suggested that the relative dominance ofindividual features affecting the probability of accuratelydiscriminating native versus decoy structures was in the order ofZEPII >main chain-main chain H-bonds >density of H-bonds >percentage ofcharged groups >density of cation-pi interactions >buried surfacearea >percentage of neutral polar groups >density of ionic bonds. Eachof the above features was found to be significant at an alpha level of0.05. Based on the logistic regression coefficients, H-bond and ionicbond density, main chain-main chain H-bonds and buried surface areaappear to be over-estimated in the docked models. This is anticipatedsince increasing the values of the above features tends to maximize thescoring function. On the contrary, ZEPII, cation-pi interactions,percentage of charged and neutral polar groups appear to beunder-represented in the docked models. Cation-pi interactions,percentage of charged and neutral polar groups do not contributesignificantly to the energy scoring function; hence these features werenot optimized in the docked interfaces. Further, assessment of dockedmodels shows that docking procedure does not faithfully recapitulate thepairwise interactions common to dissociable antigen-antibody complexes;hence the mock interfaces were found to have low ZEPII values.

Next, MLR was used to predict x-ray structures of 37 antigen-antibodyinteractions in the test data set using the pre-computed significantfeatures, and then the sensitivity of the MLR-based prediction wascompared to those of the ZRANK energy function, used in docked models(see Methods section). Overall, MLR was shown to be better at predictingx-ray structures than ZRANK energy function (FIG. 1), suggesting thatMLR approach yielded improvements over ZRANK in predicting native-likebinding poses. Closer examination of the decoy models, their ZRANKscores and MLR-based prediction probabilities revealed interestinginsights (FIG. 2). ZDOCK identified native-like structures for 29 out ofthe 37 structures indicating that computational search algorithms to bevery accurate. However, (1) ZRANK score varied significantly evenbetween structurally similar poses (FIG. 2A); (2) very differentstructures could receive approximately the same score making itdifficult to discriminate accurate from inaccurate solutions (FIG. 2A);(3) worse, inaccurate solutions often received better score thannative-like structures (FIG. 2A); (4) while MLR-based predictionprobability also varied between structurally similar poses, non-nativeposes rarely received high prediction probability indicating that thelikelihood of a false positive structure prediction was lower when theposes are ranked according to prediction probability. Accordingly,prediction probability was seen to correlate better with RMSD whencompared to ZRANK score (FIGS. 2B & 2C).

Example 2: Using Physicochemical Features for Prediction ofAffinity-Enhancing Mutations

Studies in this Example show the development of a scoring scheme fordesigning affinity enhancing mutations for protein-protein (e.g.,antigen-antibody) interactions.

Specifically, this Example describes a mathematical model developed toquantify the propensities of pairwise amino acid interactions (seeMethods section). These statistical propensities were formulated as aninteraction matrix that assigns a weight to each possible pair of aminoacids. The fitness of a residue at a CDR position, also called the aminoacid interface fitness (AIF), was the combined propensity of allinter-protein pairwise contacts (defined as two amino acids within acertain distance of each other) involving that residue. Substitutionsthat lead to an improvement in AIF value without any structuralconsequences were considered as candidates for affinity enhancement. Thepropensities were determined using statistics on amino acid contacts ina database of known protein structures (see Methods section). Avoidingmultiple distance cutoffs and energy minimization steps eliminated heavydependencies on atomic coordinates.

Consistent with the observations made by previous studies, thepropensity data showed the dominance of tyrosine, tryptophan, serine andphenylalanine over other residues in the paratope (Table 2). The AIFmetric was then used to predict affinity enhancing mutations ofantibodies across three different systems for which published datavalidated the predictions. One of the test case was the anti-EGFRantibody drug cetuximab (Erbitux), where a 10-fold affinity improvementto 52 pM was engineered by three mutations on the light chain. Two ofthese predicted mutations, S26D and T31E were shown to improve bindingaffinity as single mutations in cetuximab and closer inspection of thethird mutation (N93A) revealed that Ala is among a set of residues withweak contact propensities overall. Another test case was theanti-lysozyme model antibody D44.1, where eighteen mutations werepredicted to be suitable for affinity enhancement. Four of the predictedmutations on the heavy chain, T28D, T58D, E35S, G99D, were part of apublished high-affinity variant of D44. 1. Another test case was theantibody E2 that targets cancer-associated serine protease MT-SP1. AIFmetric predicted eight mutations which included T98R, confirming aprevious in-silico affinity enhancement study, which had identified asingle mutation T98R for improving the antibody affinity by 14-fold to340 pM.

Example 3: Design of Affinity Enhancing Mutations in Dengue Antibody

Analysis in this Example illustrates that an anti-DV antibody that bindsonly certain serotypes of DV can be modified through engineering suchthat a variant is generated that potently neutralizes activity of allfour serotypes of DV. Specifically, studies in this Example show thatrationally designed mutations in a Dengue mAb 4E11 augments its affinityfor DV serotype 4 (DV4), and do not significantly detrimentally affectits binding to DV serotypes 1-3 (DV1-3).

Binding and neutralizing activity profiles of mAb 4E11 show highaffinity and inhibitory potency to DV1-3, but low affinity andneutralizing activity to DV4 (FIG. 3). To engineer 4E11 for potentneutralization activity to all four serotypes, the design approach (FIG.4) relied on three important factors: (1) to generate an accurate modelof 4E11-EDIII interaction, (2) to understand the serotype-specificstructural elements and recapturing the determinants of affinity andspecificity, and (3) to design of substitutions which confer favorableinteraction and hence improved affinity with DV4.

In the absence of the antibody crystal structure, a structural model ofthe Fv region was built and the modeled Fv was docked against EDIII ofDV1 using ZDOCK software, and previously published functional data onthe epitope and CDR H3 paratope (Watanabe et al., 2012 Trends inMicrobiology 20:11-20) were included as specific residues in the bindinginterface to ensure docked poses did not deviate significantly from thenative complex (see Methods section). ZDOCK was run five times withdifferent combinations of input interface residues and the best rankingmodel from each run (FIG. 5) was re-ranked using MLR probabilities(Table 3). The top model predicted by the MLR approach did not matchwith the prediction of the ZRANK method.

The top model predicted by the MLR approach was validated by comparisonperformed between paratope hot spots computationally predicted by theweb server ANCHOR [Dosztanyi et al., 2009 Bioinformatics 25:2745-2746]and hot spots determined experimentally by Ala-scanning of each positionin all CDR loops of 4E11 with binding assessment by indirect ED-III(DV1) ELISA. Hot spot prediction of the selected model correctlyidentified 61% of experimentally determined hot spots, whereas theremaining poses had hot spot prediction accuracies of <45% (range28-44%), thus indicating that the selected pose was likely to reflectthe true 4E11/ED-III binding configuration.

The top 4E11-ED-III (DV1) model was used to guide the modeling of theinteraction between 4E11 and a representative EDIII strain from each ofthe other three serotypes (see Methods section). Using the fourstructural models, the mode of antibody binding to each of the serotypeswas examined and the molecular basis of poor affinity towards DV4serotype was identified using a combination of sequence and ED-IIIdomain-level structural analysis. Analysis revealed multiple amino aciddifferences within and around the 4E11 binding interface between DV4 andother serotypes. Notably, the orientation of the A-strand (residues305-308) relative to neighboring β-strands was different in DV4 owing toa localized difference at position 307 (FIG. 6). Consistent with the lowaffinity and neutralizing potency to DV4, the 4E11-EDIII (DV4) interfacepossessed smaller BSA, fewer H-bonds and salt bridge contacts.

AIF index was next applied to design mutations which enhance affinity toDV4 binding. This resulted in a set of 87 mutations spanning 23 CDRpositions. The predicted mutations included amino acids of all types.The choice of amino acid replacements were not always intuitive (e.g.,if the epitope region surrounding a paratope CDR position was negativelycharged, Arg and Lys were not always statistically favored at that CDRposition). While residues that improve energetics were favored, affinitygain might happen through improvements in electrostatic complementarity,packing and hydrophobic surface area. A conscious effort was taken indesigning affinity-enhancing mutations at CDR positions proximal to DV4serotype-specific residues (FIG. 6). Mutations that had potential toimprove DV4 affinity while not being detrimental to other serotypes weregiven higher preference. In an effort to learn about the effects ofpoint mutations on binding affinity, mutants were not restricted toresidues with the highest probabilities of success.

Example 4: Experimental Characterization of Engineered Dengue Antibody

Experiments in this Example elucidate that specific engineeredsite-directed mutations in an antibody increase its affinity and/orpotency for EDIII of DV4 without, or with only minimal reduction inbinding affinity and/or potency to EDIII of DV1-3. Experiments in thisExample also demonstrate that binding properties of engineeredantibodies can also be accurately quantified. Experiments in this studymoreover show that an engineered Dengue antibody designed by combiningspecific successful single-mutations results in maximum increase in theaffinity of the antibody. Furthermore, experiments in this Exampleconfirm that engineered antibodies designed in this study not onlyexhibit strong inhibitory activity to all four serotypes of DV, but alsohave potent antiviral activity in vivo.

A total of 87 mutations were selected for experimental testing byindirect ELISA using purified recombinant EDIII of DV1-4 as the coatedantigen. Mutants were generated by site-directed mutagenesis,sequence-confirmed, and expressed from 293 cells by transienttransfection. Ten mutations were identified with enhanced EDIII-DV4affinity with no or minimal reduction in binding to EDIII of DV1-3(Table 3). These 10 mutations spanned five CDR positions, with four inVL (R31, N57, E59, and S60) and one in VH (A55). Eight of the 10mutations were in VL, with 7 being in L2 alone. The successful mutationswere mostly charged or polar in nature, and found to reside at theperiphery of the antibody-antigen interface area (FIG. 7). Structuralanalysis showed the mutant side chains created contacts with highlyconserved epitope residues, suggesting why they were not detrimental toDV1-3 binding (FIG. 6 and Table 5).

For further accurate quantification of binding properties of these 10single-mutants discussed above, competition ELISA experiments wereperformed to determine affinities at equilibrium and in solution. Table6 outlines affinity results from five single mutant antibodies,representing those mutations which demonstrated greatest EDIII-DV4affinity enhancement while maintaining affinity to EDIII of DV1-3. Theextent of DV4 affinity enhancement ranged from 1.1-fold (VL-R31K) to9.2-fold (VH-A55E). Surprisingly, two mutations conferred increasedaffinity to other serotypes; VH-A55E resulted in a 16- and 7-foldaffinity increase to ED-III-DV2 and ED-III-DV3, respectively, whileVL-N57E demonstrated a 3-fold affinity increase to ED-III-DV2. Onlythree of the 15 affinities measured to serotypes 1-3 (with the fivesingle mutant antibodies) showed a decrease greater than 2-fold, andonly one antibody-EDIII affinity (VL-E59Q for EDIII-DV3) resulted ingreater than a 3-fold decrease in affinity.

Structurally, the five affinity-enhancing positions map to spatiallydistinct regions of the paratope (FIG. 7) suggesting that additionalenhancement could be achieved by combining successful single mutations.Multiple three-, four- and five-mutant combinations were tested, and aquintuple mutant antibody, termed 4E5A, showed the greatest increase inaffinity. Surprisingly, 4E5A was composed of five substitutionsrepresenting the amino acid change at each position which conferredgreatest affinity improvement to EDIII-DV4 as a single mutant. Comparedto the parental mAb, 4E5A displayed 450-fold affinity improvement toEDIII-DV4 (K_(D)=91 nM) while maintaining affinity to EDIII of DV1 andDV3 and a 15-fold affinity increase to DV2 (Table 7 and Table 8).Significantly, these results illustrated that affinity of an antibodycould be increased from micromolar to near-nanomolar affinity. SurfacePlasmon Resonance (SPR) was used to verify affinity measurements as wellas obtain kinetic binding parameters (Table 9 and FIG. 8). Affinityvalues from SPR were in good quantitative agreement with those obtainedby competition ELISA, with the exception that specific binding of 4E11WT to EDIII-DV4 could not be detected, indicating a very low affinity,which was in general agreement with competition ELISA results (K_(D)=41μM).

To determine whether increased affinity of 4E5A to EDIII-DV4 translatedto enhanced activity, a focus reduction neutralization test (FRNT) assaywas used. Compared to WT 4E11, 4E5A showed a >75 fold increase inneutralizing potency towards DV4, and it maintained potency to DV1-3(FIG. 9). 4E5A showed strong inhibitory activity to all four serotypes,with FRNT₅₀ values of 0.19, 0.028, 0.77, and 4.0 μg/ml for DV1-4,respectively. To further elucidate 4E5A activity, the antibody wasassessed in an AG129 mouse model of DV2 challenge, which shows peakviremia at day 3 post-infection. At both 1 mg/kg and 5 mg/kg, 4E5Ademonstrated a significant reduction in viremia, with 5 mg/kg treatmentresulting in virus titer levels below the limit of detection (FIG. 10).Collectively, these results showed that the engineered mAb 4E5Aexhibited strong inhibitory activity to all four serotypes of DV and hadpotent antiviral activity in vivo.

Engineered antibodies that can be designed based on this study (e.g.,4E5A) represent important drug candidates and additionally can be takenup for further rounds of affinity maturation and humanization as isknown in the art. The crystal structure of 4E11/ED-III complex waspublished prior to submission of the present patent application, whichallowed comparison of the structural model discussed in this study withthe published complex structure and indeed, excellent correspondencebetween the two structures with C-alpha RMSD value of 1.4 angstrom wasobserved, further confirming the significance of this study.

Discussion

Traditional approaches for discovering antibodies of therapeuticinterest rely on experimental methods such as phage-display techniques.However, these approaches are expensive, technically challenging andtime consuming. For instance, the influenza FI6 mAb, which neutralizesclade 1 & 2 viruses, was identified by screening 104,000 B cells. Analternate strategy would be to modify the properties of an existingantibody via rational engineering. In this study, computational methodsfor ab initio modeling and antibody re-design were presented. In testruns, the sensitivity of the MLR prediction method in picking X-raystructures (out of several decoy models) appeared superior to ZRANK.Further, it was shown that the AIF metric could capture known affinityenhancing mutations across multiple systems. This framework was thenapplied to engineer broader specificity and affinity to an anti-Dengueneutralizing mAb. The results obtained by this study were important as:(1) only few studies have attempted to improve the cross-reactivity ofan antibody; (2) this is the first study that has employed an empiricalapproach towards antibody re-design and affinity enhancement; and (3)affinity enhancing mutations were predicted without the crystalstructure of the antibody-antigen complex (aka blind prediction). Thisstudy showed for the first time that application of a computationalapproach led to a greater than ˜400-fold improvement in affinity of anantibody (Table 10). Given the simplicity of these computationalmethods, they could be broadly employed for antibody engineering, andunlike physics-based energetic approaches, they are not affected by theprecise location of the atom coordinates of the starting structure.

The top docking solution from ZRANK was structurally very different fromthe native-structure, indicating that any affinity enhancement effortsfollowing the top ZRANK model would not have led to fruitful results.Affinity enhancing mutations were also predicted using the X-raystructure by energetics approach and results highlighted the challengesin discriminating stabilizing and neutral mutations (Table 11). Moresignificantly the affinity enhancing mutations N57E, N57S and E59N wereclassified as destabilizing (Table 11). Since ZRANK is widely used andhas shown considerable success in the CAPRI experiments, the methodpresented in this study would perform comparatively well when stackedagainst other docking algorithms. The fact that ZEPII appearedsignificantly, indicated that amino acid composition and inter-residuecontacts contained discriminatory power. Interestingly, some geometricalfeatures also have the predictive power to discriminate nativeinterfaces from decoys. This correlated with the observation made byprevious studies that antigen-antibody interfaces were more planar andsignificantly well-ordered or packed. Between the different combinationsof interface residues that were used to generate the five differentmodels, the accurate model was produced by using all the known epitopeand paratope interface residues as adding more context narrowed thesearch space and therefore increased the chances of finding anear-native complex structure.

Phage display and directed evolution methods randomized select CDRloops, especially VH-CDR loops since they accounted for most of thestabilizing contacts. The results on 4E11 showed that diversificationstrategies must use a rational approach and involve VL-loops fortargeted diversification. The observation that affinity enhancingmutations were mainly polar in nature and were present at the peripheryof the binding interface was consistent with known data. It is likelythat these mutations increased the association rate by increasing theefficiency of collision. The success rate in predicting mutations withtargeted activities is 12% (10/87). These results were encouraging giventhe complexity of the design problem (i.e. involvement of multipleantigens) and considering that random mutations would have in average adetrimental effect on binding affinity.

Studies have shown that murine germline harbors gene segments with aninherent capacity for high-affinity binding to EDIII domain (Ref 24,32). Despite the beneficial effect of the 5 mutations, these mutationshave not co-evolved in vivo. Codon-level analysis showed that amino acidreplacements at N57E and S60W required at least two base changeshighlighting the limitations at the genomic level. Previous studies haveshown that the epitopes recognized by anti-DV antibodies fall into threedifferent regions: (1) lateral-ridge epitope on ED-III(serotype-specific potent neutralizers); (2) A-strand of DIII(subcomplex-specific neutralizers); and (3) other DII and DIII epitopes(complex-specific or flavivirus cross-reactive moderately potentneutralizers). In this study, it was shown for the first time thatantibody against A-strand epitope could be engineered to bind all fourserotypes with good in vitro potency. Collectively, 4E5A exhibited aninteresting broad spectrum neutralization profile and would be anantibody of interest for potential therapeutic development for treatmentof Dengue disease. mAb therapeutics against DV in humans could faceregulatory hurdles due to antibody-dependent enhancement. However,recent studies have shown that modifications to the Fc region ofrecombinant anti-DV antibodies prevent ADE in vivo, thus presentingopportunities for these newer complementary approaches. The degree ofconservation of mAb epitope can be a significant factor in determiningneutralizing spectrum and in vivo protection. Phylogenetic analysis ofDV4 viruses has revealed the existence of four distinct genotypes: I(Southeast Asia), II (Indonesia), III and IV (Sylvatic or Malaysia).Within genotype II, viruses cluster into two distinct clades previouslydefined as IIa and IIb. Sequence analysis of 4E11-5A's epitope regionrevealed high degree of conservation in genotypes IIa, IIb and 4, whilerelatively lower conservation in genotype I, suggesting to the presentinventors that the engineered antibody would likely be effective againstthe majority of DV4 viruses.

TABLE 1 Description of physicochemical features. Feature No. Descriptionof feature Feature sub-classification Chemical 1 Number of various typesof interactions (1) hydrophobic, (2) disulphide bridges, (3) hydrogenbond, (4) ionic interactions, (5) aromatic-aromatic, (6)aromatic-sulphur, (7) cation-pi 2 density of each type of interactions(i.e. how (1) hydrophobic, (2) disulphide many contacts of each type isobserved on bridges, (3) hydrogen bond, (4) ionic average per 100 squareangstroms of the interactions, (5) aromatic-aromatic, interface) (6)aromatic-sulphur, (7) cation-pi 3 classification of hydrogen-bonds (1)main chain - main chain, (2) main chain - side chain, (3) side chain -side chain) 4 number of salt bridge interactions 5 number of hydrogenbonds that involve charged residues 6 composition of chemical groups (1)polar, (2) neutral and (3) non- polar chemical groups 7 ZEPII Assessesthe frequencies of favorable interactions to indicate the probability ofantibody binding to a given surface (see Methods section) Physical 7buried surface area 8 planarity 9 surface complementarity 10 interfaceatom packing density 11 distance between the binding site of the antigenfrom its center of mass 12 novel metric that quantifies the antibodybinding potential of a surface by enumerating the number of favorableinteractions that are common to antigen-antibody interfaces

TABLE 2 The 20X20 amino acid propensity matrix. Paratope amino acids areindicated on the left side and epitope amino acids are indicated on theupper side. The propensity data was generated using 77 non-redundantantigen-antibody complexes. ALA ARG ASN ASP CYS GLU GLN GLY HIS ILE LEUALA 0.25 0.59 0.14 0.53 0 0.28 0.6 0.35 1.33 0.68 1.1 ARG 0.58 0.87 1.112.29 0 1.75 0.87 0.67 0.95 1.03 0.99 ASN 0.74 1.32 1.04 0.94 0.72 1.281.32 1.08 1.94 1.03 0.33 ASP 0.23 1.68 0.81 0.6 0 0.75 0.54 0.79 1.040.4 1.27 CYS 5.29 0 0 5.59 36.02 0 0 2.46 0 0 0 GLU 0.22 1.41 0.6 0.23 00.36 0.39 0.2 0.57 0.39 0.14 GLN 0.44 0.2 0.72 0.23 0 0.48 0.26 0.61 00.78 0.82 GLY 0.31 1.01 0.57 0.49 1.06 1.37 0.99 0.72 0.68 0.56 0.39 HIS0.55 0.64 0.76 0.87 0 0.91 1.15 0.51 0.73 0.49 0.52 ILE 0.31 0.57 0.170.32 0 0.34 0.73 0.14 1.2 0.55 1.33 LEU 0.42 0.88 0.7 0.22 0.72 0.7 0.630.59 1.12 1.51 1.98 LYS 0 0.31 0.37 0.71 0 1.86 0.4 0.16 0.89 0 0.42 MET0 0.99 1.17 0 0 1.17 0.64 0.5 1.4 0.95 0 PHE 1.81 1.36 0.74 0.72 0.770.87 1.22 1.16 2.98 0.81 1.41 PRO 0.75 1.04 0.41 0.2 0 0.41 1.12 0.171.97 1 1.4 SER 1.12 1.27 0.62 0.93 1.37 1.64 1.54 0.6 1.16 0.43 1.25 THR0.84 1.17 0.79 1.14 0 1.06 1.15 0.34 1.42 0.54 0.37 TRP 1.27 1.71 1.161.05 3.37 0.47 2.03 0.99 0.261 0.51 1.06 TYR 1.48 2.21 1.83 1.56 2.041.96 1.6 1.73 2.01 1.9 2.38 VAL 0.3 1.1 0.49 0.78 1.01 1.3 0.88 0.281.56 0.79 1.11 LYS MET PHE PRO SER THR TRP TYR VAL ALA 0.33 2.3 2.940.77 0.25 0.38 1.49 0.59 1 ARG 0.44 0.79 0.75 0.15 0.5 0.66 0.29 2.240.57 ASN 1.05 1.53 0.54 0.74 0.78 0.58 0.83 0.82 0.41 ASP 2.2 0.62 0.580.51 0.84 1.08 0.89 1.05 0.27 CYS 0 0 6.85 2.68 0 0 0 0 4.17 GLU 0.850.39 0.56 0.44 0.75 0.55 0.85 0.17 0.34 GLN 0.38 0 0.57 0.44 0.65 0.44 01.02 0 GLY 0.9 0.76 0.94 0.89 0.51 0.84 0.61 0.97 0.74 HIS 0.6 1 0 0.840.27 0.56 0 0.43 0.65 ILE 0.66 2.22 1.58 0.31 0.45 0.92 3 2.36 1.2 LEU0.83 1.16 1.37 0.86 0.52 0.43 2.09 1.64 1 LYS 0.59 0 1.31 0.17 0.67 0.171.33 0 0.27 MET 0 3.88 0 0.54 0 0 2.1 1.65 0.84 PHE 1.17 0.82 2.05 1.490.67 1.03 1.78 0.35 1.6 PRO 0.49 2.72 1.94 0.38 0.55 0.57 0.74 1.16 0SER 0.97 1.02 1.04 0.73 0.83 0.93 1.42 1.43 0.82 THR 0.83 1.31 0.16 0.790.77 1.03 0.24 0.56 0.76 TRP 1.78 1.03 0.73 1 1.12 0.86 0.56 1.86 1.56TYR 1.78 1.89 2.69 1.88 1.35 1.21 1.4 1.36 1.46 VAL 0.26 0.54 1.15 0.30.59 0.45 2.92 0.69 0.47

TABLE 3 Physicochemical properties of the top five docked structuralmodels. Columns 2-9 provide values of pre-computed significant featuresfor the docked models. The p-value and odds ratio (OR) are listed in thecolumn headers. The MLR regression coefficient of the features is listedin the last row of the table. Columns 10 and 11 provide MLR-basedprediction probability and ZRANK score, respectively. Main chain- IonicHydrogen main contact Cation-pi bond chain ZEPII BSA density densitydensity contacts (OR = (OR = (OR = (OR = (OR = (OR = 4.948081868;0.595234401; 0.769203281; 1.453682511; 0.409261894; 0.072352881; p-value= p-value = p-value= p-value p-value p-value Pose 2E−16) 0.000994)0.048709) 0.000831) 0.000000432) 3.06E-11) 1 1.1032203 2269 0.485 0.1760.661 15 2 1.0727273 1941 0.567 0.155 0.824 16 3 1.1028767 2340 0.5130.128 1.026 24 4 1.0836066 2436 0.369 0.164 0.698 17 5 0.9682895 24810.363 0.202 0.846 21 Regression 1.599 −0.5188 −0.2624 0.3741 −0.8934−2.6262 coefficient Percentage Percentage of of neutral charged polargroups groups (OR = (OR = 4.853984917; 1.412696091; MLR p-value p-valueprediction ZRANK Pose 0.000000516) 0.03383) probability score 1 100.1071 0.00263 −75.833 2 15 0.0982 0.00159 −85.636 3 19 0.1389 0.00003−66.759 4 14 0.1186 0.00192 −71.73 5 16 0.1587 0.00001 −72.775Regression 1.5798 0.3455 coefficient

TABLE 4 Mutations that led to increase in EDIII-DV4 affinity whilemaintaining original EDIII-DV1-3 affinity. Chain CDR Position WT residueMutation VH H2 55 Ala Glu VH H2 55 Ala Asp VL L1 31 Arg Lys VL L2 57 AsnGlu VL L2 57 Asn Ser VL L2 59 Glu Gln VL L2 59 Glu Asn VL L2 60 Ser TrpVL L2 60 Ser Tyr VL L2 60 Ser Arg

TABLE 5 Contacts made by affinity enhancing mutations. Predicted DV4Chain & CDR Position WT residue Mutation contacts VH - H2 55 Ala GluH-bond, Ionic contact with Lys (310), Lys (323) Asp H-bond, Ioniccontact with Lys (310), Lys (323) VL - L1 31 Arg Lys Ionic contact withGlu (311) VL - L2 57 Asn Glu Ionic contact with Lys (305) Ser H-bondwith Lys (310) VL - L2 59 Glu Gln H-bond with Glu (327) Asn H-bond withGlu (327) VL - L2 60 Ser Trp Hydrophobic contact with Ala (329) TyrH-bond with Glu (327) Arg Ionic, H-bond with Glu (327) and H-bond withGly (328)

TABLE 6 Affinities of single mutant antibodies with increased EDIII-DV4affinity and similar EDIII-DV1-3 affinities relative to 4E11 WT.Mutations included are those which, for each identified position,demonstrated greatest EDIII-DV4 affinity while approximately maintainingEDIII-DV1-3 affinity. K_(D) values represent the average of at least twoindependent experiments. Muta- EDIII-DV1 EDIII-DV2 EDIII-DV3 EDIII-DV4tion CDR K_(D) (nM) K_(D) (nM) K_(D) (nM) K_(D) (nM) 4E11 — 0.328 5.2021.8 40,793 WT A55E H2 0.295 0.323 2.95 4442 R31K L1 0.378 5.35 21.137,292 N57E L2 0.281 1.75 33.9 8408 E59Q L2 0.772 10.8 102 11,034 S60WL2 0.284 6.30 23.1 26,351

TABLE 7 Affinity of combination mutant 4E11-5A. EDIII-DV1 EDIII-DV2EDIII-DV3 EDIII-DV4 K_(D) Fold- K_(D) Fold- K_(D) Fold- K_(D) Fold-Method mAb (nm) change (nM) change (nM) change (nM) change Competition4E11 0.328 — 5.20 — 21.8 — 40,793 — ELISA WT 4E11- 0.309 1.1 0.246 21.116.5 1.3 91.2 447.3 5A SPR 4E11 0.50 — 6.20 — 7.58 — NB — WT 4E11- 1.780.28 0.70 8.9 5.19 1.5 114 — 5A

TABLE 8 Energetic calculations of 4E5A showing mutations have additiveeffect on binding energy. EDIII−DV4 ΔG EDIII−DV4 ΔΔG Antibody(kcal/mol)^(a) (kcal/mol)^(b) 4E11 WT −5.98 — VH-A55E −7.29 −1.31VL-R31K −6.03 −0.05 VL-N57E −6.92 −0.93 VL-E59Q −6.76 −0.77 VL-S60W−6.24 −0.26 4E5A −9.59 −3.61 ^(a)Free energy calculated by ΔG =RTln(K_(D)) at 25° C. ^(b)ΔΔG = ΔG_(mutant) − ΔG_(WT)

TABLE 9 Kinetic binding parameters for 4E11 and 4E5A measured by SPR.EDIII-DV1 EDIII-DV2 EDIII-DV3 EDIII-DV4 k_(on) ^(a) k_(off) ^(b) k_(on)^(a) k_(off) ^(b) k_(on) ^(a) k_(off) ^(b) k_(on) ^(a) k_(off) ^(b) 4E111.11 5.51 1.98 123 1.34 102 N.B.^(c) N.B.^(c) 4E5A 1.17 20.8 2.01 14.12.76 143 0.766 875 ^(a)k_(on) values are expressed as (×10⁶ M⁻¹s⁻¹)^(b)k_(off) values are expressed as (×10⁻⁴ s⁻¹) ^(c)N.B., no binding

TABLE 10 Comparison of results of various in silico antibody affinityenhancement studies. Crystal Single/multi Affinity Study Method AntibodyAntigen structure? antigen improvement Our study Empirical 4E11 DengueNo Multi ~450 informatics gpE Lippow SM Energetics D44.1 lysozyme YesSingle 140 et. al., Nature Biotech (2007) Marvin J.S. Energetics Y0101VEGF Yes Single ~6 et. al., Biochemistry (2003) Clark LA Energetics AQC2VLA1 Yes Single ~10 et. al., Protein Science (2006) Farady et al.Energetics E2 Protease Yes Single 14 (2009) MT-SP1 Bioorg. Med. Chem.Lett.

TABLE 11 Antibody mutations predicted using energetics approach.Mutations that increased the affinity of 4E11 are bolded and underlined.Mutation Mutation Effect Mutation Effect Mutation Effect at on of atMutation of at Mutation of ALA55 Energy Mutation ARG31 Energy MutationASN57 Energy Mutation VH:ALA55 VL:ARG31 VL:ASN57 GLU − 1    stabilizingLYS − 1.01 stabilizing LEU −1.79 stabilizing THR −0.44 neutral HIS −0.13neutral PHE −1.69 stabilizing TRP −0.4  neutral MET −0.04 neutral TYR−1.44 stabilizing ASP − 0.37 neutral PRO −0.04 neutral ARG −0.88stabilizing GLN −0.33 neutral ARG 0   neutral TRP −0.64 stabilizing LEU−0.33 neutral ILE   0.16 neutral GLN −0.62 stabilizing TYR −0.29 neutralTHR   0.22 neutral MET −0.57 stabilizing ARG −0.23 neutral VAL   0.22neutral HIS −0.51 stabilizing PRO −0.23 neutral ASN   0.24 neutral LYS−0.04 neutral ILE −0.17 neutral ALA 0.3 neutral ASN 0   neutral MET  0.17 neutral CYS   0.32 neutral ILE   0.53 destabilizing VAL −0.14neutral SER   0.34 neutral ASP   0.58 destabilizing PHE −0.09 neutralGLY   0.41 neutral PRO   0.68 destabilizing CYS −0.04 neutral TYR   0.46neutral THR   0.93 destabilizing ALA 0   neutral PHE   0.47 neutral CYS  1.14 destabilizing HIS   0.06 neutral GLN   0.48 neutral GLU    1.17destabilizing GLY   0.07 neutral LEU   0.48 neutral ALA   1.32destabilizing ASN   0.13 neutral TRP   0.68 destabilizing SER    1.53destabilizing SER   0.17 neutral ASP   1.14 destabilizing VAL   1.88destabilizing LYS   1.06 destabilizing GLU   1.26 destabilizing GLY  1.95 destabilizing Mutation Effect Mutation Effect at Mutation of atMutation of GLU59 Energy Mutation SER60 Energy Mutation VL:GLU59VL:SER60 PHE −1.02 stabilizing SER −2.21 stabilizing TYR −1  stabilizing PHE −2.17 stabilizing GLN − 0.86 stabilizing ARG − 1.69stabilizing ARG −0.5  neutral LYS −1.69 stabilizing LYS −0.35 neutralGLN −1.65 stabilizing ASP −0.29 neutral LEU −1.44 stabilizing MET −0.24neutral TRP − 1.31 stabilizing HIS −0.23 neutral MET −1.26 stabilizingLEU −0.1  neutral HIS −0.8  stabilizing ILE −0.01 neutral ASN −0.79stabilizing GLU 0   neutral CYS   0.64 stabilizing PRO   0.05 neutralTHR −0.57 stabilizing VAL   0.06 neutral ALA −0.56 stabilizing THR  0.17 neutral ASP −0.45 neutral SER   0.34 neutral GLU −0.42 neutralCYS   0.39 neutral GLY −0.05 neutral ALA   0.51 destabilizing TYR 0   neutral GLY   0.52 destabilizing ILE   0.43 neutral ASN    0.68destabilizing VAL   0.61 destabilizing TRP   2.53 destabilizing PRO  3.31 destabilizing

Methods

A Mathematical Model for Estimating Contact Propensities of Amino Acidsin the Antigen-Antibody Interface

Briefly, in an antigen-antibody interface, a pair of residues presumablyinteract if they had favorable energetics of interaction or by chanceoccurrence. The propensity of amino acid interaction was calculated bycomputing the number of interactions expected by chance i.e. theexpected frequency, and dividing the observed frequency by this number.

If two amino acids, one from each side of the antigen-antibodyinterface, were within 4.5 Å (i.e. shortest non-H atom distance is lessthan 4.5 Å) from each other, they were defined as pair residues. If thetotal number of pairwise interactions between residues x (antigen) and y(antibody) at the interface was N (x, y), then their concurrencefrequency, F (x, y), was defined as follows:

${F\left( {x,y} \right)} = \frac{N\left( {x,y} \right)}{\sum\limits_{l = 1}^{20}{\sum\limits_{m = 1}^{20}{N\left( {l,m} \right)}}}$

The denominator of the above equation indicates the summation ofpairwise interactions of all residue pairs in the interface.

The frequency of occurrence of every amino acid at paratope and epitopemust be calculated. The frequency of a particular amino acid x in theepitope, F^(epitope)(x), was defined as follows:

${F^{epitope}(x)} = \frac{N(x)}{\sum\limits_{l = 1}^{20}{N(l)}}$

In the above equation N(x) denotes the count of amino acid x in theepitope. The denominator represents the total number of all amino acidsin the epitopes.

Similarly, the frequency of occurrence of amino acid y in the paratope,F^(paratope) (y), was defined as follows:

${F^{paratope}(y)} = \frac{N(y)}{\sum\limits_{l = 1}^{20}{N(l)}}$

In the above equation, N(y) denotes the number of amino acid y in theparatope. The denominator indicates the total number of all amino acidsin the paratopes.

Parameters F (x,y), F^(epitope)(x) and F^(paratope)(y) were determinedusing all the seventy-seven benchmarked antigen-antibody structures inthe data set. Consistent with observations made by previous studies,tyrosine, serine, glycine and asparagine were the most abundant paratoperesidues whereas lysine, arginine, leucine and glycine were the mostabundant epitope residues (FIG. 11). If the occurrences of amino acids xand y were independent, EF^(epitope-paratope) (x, y) defined in thebelow equation was an expected frequency rate that amino acids x and yappear concurrently.

EF(x,y)=F ^(epitope)(x)F ^(paratope)(y)

If the concurrence rate of the amino acids x and y at the interface forthe antigen was more than the expected rate, the following ratioRA_(a)(x, y) becomes greater than 1.

${{RA}\left( {x,y} \right)} = \frac{F\left( {x,y} \right)}{{EF}\left( {x,y} \right)}$

RA_(s)(x, y) was a 20×20 matrix. Exemplary applications of RA_(s)(x, y)are suggested below.

Using RA (x, y) to determine the AIF of a CDR residue. The AIF of a CDRresidue in the interface was defined as the sum of the RA (x, y) withits neighbors. Neighbors were defined by a distance criterion (4.5 Å).

Determine the optimal choice of amino acid at an interface position(paratope re-engineering). Given an antigen-antibody complex, amino acidpreferences at a CDR position were computed using the contact potentialscore. Specifically, at a given CDR position, the wild type (WT) residuewas systematically substituted by the remaining amino acids excludingglycine and proline (to avoid backbone conformation alterations) and theprobability of replacement was evaluated at each instance using the AIFmetric. Single mutations with replacement potential higher than wildtype residue were reevaluated computationally to find mutations that—(a)do not bury polar groups, and (b) do not cause steric hindrance.

Using RA (x, y) to quantify the strength of interaction ofantigen-antibody interface (the Epitope-Paratope Interface Index). Theinteraction between an antigen and antibody results from the formationof numerous non-covalent bonds. Therefore, the interaction affinity wasdirectly related to summation of the attractive and repulsive forces(van der Waals interactions, hydrogen bonds, salt bridges andhydrophobic force). Herein, the strength of interaction of anantibody-antigen interface was investigated quantitatively by a linearcombination of RAs for all combinations of amino acid pairs. An indexexpressing the strength of an antigen-antibody interface ‘i’ (calledEpitope-Paratope Interface Index (EPII)) was defined by:

${EPII}_{i} = \frac{\sum\limits_{x = 1}^{20}{\sum\limits_{y = 1}^{20}{{F^{i}\left( {x,y} \right)}{{RA}\left( {x,y} \right)}}}}{\sum\limits_{x = 1}^{20}{\sum\limits_{y = 1}^{20}{F^{i}\left( {x,y} \right)}}}$

In the equation above F^(i) (x, y) denotes the concurrence frequency ofamino acids x (x belongs to secondary structural groups) and y atinterface i.

Using EPII to discriminate a true antigen-antibody interaction fromdocking decoys. In order to distinguish an interface with the mostpotential from other decoy interfaces generated by computationaldocking, the EPII values should be normalized by all the interfaces inthe protein. Z-scored EPII were used for this purpose. If M interfaceswere found in a protein, the Z-scored EPII for interface i wascalculated as follows:

${Z_{{EPII}_{i}} = \frac{{EPII}_{i} - \mu}{\sigma}},{where}$$\mu = \frac{\sum\limits_{i = 1}^{M}{EPII}_{i}}{M}$$\sigma = \sqrt{\frac{\sum\limits_{i = 1}^{M}{\left( {{EPII}_{i} - \mu} \right)*\left( {{EPII}_{i} - \mu} \right)}}{M}}$

The Z_(EPII) _(i) score was an indicator of the probability of antibodybinding to a given interface. Interface with the highest Z_(EPII) _(i)Score (or with Z_(EPII) _(i) above the consensus value established forantigen-antibody interaction (discussed above)) in a protein was themost probable site for antibody binding.

Data Set of Non-Redundant Antigen-Antibody Structural Complexes andComputational Docking to Generate Decoy Models

A total of 568 antigen-antibody complexes from the Protein Data Bankwere analyzed. In order to ensure proper enumeration of geometricinterface features (planarity, buried surface area etc.), structureswherein the antigen length was less than 20 amino acids were excluded.Additionally, many structures contained same or similar antigen, whichcould bias the studies, giving higher weight for factors derived frommultiply-represented protein antigen. To remove redundant structuresfrom the data set, structures that have homologous antigen (defined byBLAST_ENREF_40 P-value 10e27) and share 50% epitope residues wereclassified under the same group and the structure with the highestresolution was selected as the representative. This led to seventy-sevennon-redundant antigen-antibody complex structures.

ZDOCK was used to generate decoy computational models ofantigen-antibody interaction. The protocol for generating the decoysmodels were the same for all the seventy seven structural complexes.Only the variable domain of the antibody was used for docking. Thelarger of the two molecules was considered the receptor while thesmaller molecule was considered the ligand. The ligand orientation wasrotated 6 degrees at each step to sample the various conformations.Since, the initial docking procedure explores a relative large area,distance constraints between putative hotspot residues on epitope andparatope were set up to ensure the generated models did not shiftsignificantly from the native pose. Two hotspot residues were selectedon either side to ensure the challenges faced with structure predictionwas equivalent to the 4E11 scenario. In all the decoys models, theputative epitope and paratope hotspots were within 10 angstroms fromeach other. Hotspots were identified using the web server, ANCHOR. Theinitial docking procedure generated 2,000 poses which were thenclustered based on an all-versus-all RMSD matrix, described previously.The RMSD between two docked poses was calculated based on the ligandresidues within 7 angstroms of the binding interface. Docked proteinposes representing the cluster centers were considered as decoy models.ZDOCK uses shape complementarity along with desolvation andelectrostatic energy terms (‘ZRANK’) to rank the docked poses. Each ofthese decoys was further refined using CHARMm minimization.

The X-ray structures were combined with the decoy models for evaluatingthe sensitivity of the prediction methods.

Homology Modeling of 4E11 Fv

Structural model of 4E11 Fv was built using SIWW-MODEL homology modelingserver. Studies indicated that the overall accuracy of modeling thehypervariable CDR was appropriate when (1) the degree of sequencesimilarity between the target and the template was high, (2) main-chainconformations of the CDR loops L1, L2, L3, H1, H2 follow the “canonicalstructure” and (3) heavy chain CDR3 (H3) was not unusually long.

Computational Docking for Generating 4E11-EDIII (DV1-4) Poses

The modeled Fv was docked against EDIII of a select DV1 strain usingZDOCK. DV1 antigen was used because mAb 4E11 was originally isolatedfrom a mouse infected with a DV1 virus. The structure of the DV1 antigenwas modeled using SWISS MODEL homology modeling server keeping thesolved crystal structure of DV1 EDIII (PDB: 3IRC) as the template. ZDOCKuses shape complementarity along with desolvation and electrostaticenergy terms (‘ZRANK’) to rank the docked poses. In order to ensure thedocked poses do not deviate significantly from the native complex,mapped epitope and paratope residues found in the literature were forcedto be included in the binding interface. Residues included in theinterface were 307K, 389L and 391W (epitope; DV1 numbering as in 3IRC)and 101W, 102E (paratope; numbering based on sequence position).

The structures of 4E11 in complex with DV 2, 3, 4 (EDIII) were modeledusing 4E11-DV1 EDIII structural model as the template.

Example 5: Experimental Characterization of Modified Dengue Antibody

Experiments in this Example elucidate that specific engineeredsite-directed mutations in an antibody increase its affinity and/orpotency for EDIII of DV4 without, or with only minimal reduction inbinding affinity and/or potency to EDIII of DV1-3. Experiments in thisExample also demonstrate that binding properties of engineeredantibodies can also be accurately quantified. Experiments in this studymoreover show that an engineered Dengue antibody designed by combiningspecific successful single-mutations results in maximum increase in theaffinity of the antibody.

E45A has five mutations, 4 in the light chain (VL) and one in the heavychain (VH) (SEQ ID NO. 30 and 29) compared to the predecessor antibody4E11 (SEQ ID NO. 2 and 1). These mutations provide a gain-of-function interms of binding to DENV-4 as well as increasing binding/neutralizationof DENV-3. In sequence listings below, CDRs are underlined and sites ofmutation are bold and with larger lettering.

SEQ ID NO. 1 EVKLLEQSGAELVKPGASVRLSCTASGFNIKDTYMSWVKQRPEQGLEWI GRIDP

NGDTKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYC SRGWEGFAYWGQGTLVTVSASEQ ID NO. 2 ELVMTQTPASLAVSLGQRATISCRASENVD

YGNSFMHWYQQKAGQPP KLLIYRAS

L

GIPARFSGSGSRTDFTLTINPVEADDVATYFCQR SNEVPWTFGGGTKLEIKR SEQ ID NO. 29EVKLLEQSGAELVKPGASVRLSCTASGFNIKDTYMSWVKQRPEQGLEWI GRIDP

NGDTKYDPKFQGKATITADTSSNTAYLHLSSLTSGDTAVYYC SRGWEGFAYWGQGTLVTVSASEQ ID NO. 30 ELVMTQTPASLAVSLGQRATISCRASENVD

YGNSFMHWYQQKAGQPP KLLIYRAS

L

GIPARFSGSGSRTDFTLTINPVEADDVATYFCQR SNEVPWTFGGGTKLEIKR

To further enhance the activity of 4E5A, a series of mutants wereconstructed (Table 12) and tested for binding to DENV1-4 by ELISA, SPRand as single chain constructs on yeast. One mutant, VH_S26_del, wastested for in vitro activity.

TABLE 12 Antibody mutations based on 4E5A. Antibody Designation LocationMutation 4E5A None VH_A25_del Heavy chain Deletion of Ala25 VH_S26_delHeavy chain Deletion of Ser26 VH_G27_del Heavy chain Deletion of Gly27VH_G27A Heavy chain Gly27 → Ala VH_G27P Heavy chain Gly27 → Pro VH_Y106RHeavy chain Tyr106 → Arg

Methods

Antibody Expression and Purification

Recombinant expression of antibody was carried out in HEK 293-FFreeStyle suspension cells (Invitrogen, Carlsbad, Calif.) cultured in293-F FreeStyle Expression Medium (Invitrogen, Carlsbad, Calif.)maintained at 37° C., 80% humidity and 8% CO₂. Cells (with >95%viability) were transfected with Poly-ethylene-imine Max (PEI-MAX,PolySciences) with equivalent amounts of HC and LC containing plasmids.Seven days post-infection, the cells were harvested by spinning thecells at 4000 rpm for 15 min at 4° C. and filtered through a 0.45 μmfilter system (Nalgene). The antibody was purified from the supernatantusing a Protein A linked resin (GE HiTrap Protein A HP columns on a AKTAPurifier FPLC system. The antibody was eluted with a 100 mM Glycine-HClbuffer (pH 2.5) buffer and pH neutralized by the addition of 10% 1 MTris-base with 1 M NaCl (pH 8.5). The purified sample was then bufferexchanged into 1×PBS (pH 7.4) and concentrated byultrafiltration/diafiltration (UF/DF) using a 30 KDa MWCO spin filter(Millipore). Purified antibody was quantified using NanoDropspectrophotometer.

Competition ELISA

The affinities of antibodies to EDIII, in solution at equilibrium, weredetermined by competition ELISA (1). In 96-well plates, serial dilutionsof EDIII were mixed with antibody at 0.1 nM in PBS-TB (PBS containing0.01% Tween-20 and 0.01% BSA). The mixtures were incubated overnight toallow equilibrium to be reached. Subsequently, an optimized EDIIIindirect ELISA was performed to measure the concentration of unbound orsingly bound antibody. The conditions of the ELISA were developed suchthat antibody concentration is linearly proportional to absorbance andthat the equilibrium is not significantly disturbed, conditionsimportant for obtaining accurate results (1). Maxisorp plates coatedwith EDIII-DV1 (2.5 ng/well, 4° C. overnight) were blocked with PBS-TBcontaining 1% BSA for 1 hour. After washing wells with PBS-TB,equilibrium antibody-EDIII mixtures were added to the wells andincubated for 20 min. After washing, bound antibody was detected byincubation with diluted HRP-conjugated rabbit anti-human IgG (JacksonImmunoResearch) for 1 hour, followed by addition of TMB substrate (KPL).The reaction was stopped with 1N sulfuric acid, and OD450 wasdetermined. The data were fit, by least squares regression in Excel(Microsoft), to the following model derived from mass action and asdescribed (2), with adjustment to take into account antibody bivalence(3):

$A_{i} = {{\left( {A_{\max} - A_{o}} \right) \times \frac{\sqrt{u^{2} + {4{K_{D}\lbrack{mAb}\rbrack}_{o}} - u}}{{2\lbrack{mAb}\rbrack}_{o}} \times \left( {\frac{w - \sqrt{w^{2} - {{4\lbrack{EDIII}\rbrack}_{i}{mAb}_{o}}}}{{2\lbrack{mAb}\rbrack}_{o}} + 1} \right)^{- 1}} + {A_{o}\mspace{14mu} {where}}}$  u = [EDIII]_(i) − [mAb]_(o) + K_(D)  and  w = [EDIII]_(i) − [mAb]_(o) + K_(D)

Surface Plasmon Resonance

The binding affinities and kinetics of interaction of the Dengue mAbs toEDIII were assessed by SPR using a Biacore 3000 (GE Healthcare)instrument. Briefly, goat anti-human IgG Fc polyclonal was immobilizedon carboxymethylated dextran CM5 sensor chips by amine coupling as permanufacturer's instructions. The analyses were performed at 25° C. withPBS containing 0.05% surfactant P20 and 0.5M EDTA pH 8.5 as runningbuffer. The antibodies were captured in an individual flow cell at aflow rate of 10 l/min. Injection time was varied for each antibody toyield approximately 240-280 RU of antibody captured for each cycle.EDIII from DV1, DV2, DV3 and DV4 diluted in running buffer(concentration ranging from 0.78 nM to 50 nM) or buffer alone wasinjected sequentially over a reference surface (no antibody) and theactive surface (test antibody) for 250 sec at 60 l/min. The dissociationphase was monitored for 600 sec. The surface was then regenerated withtwo 30-seconds injection of 10 mM Glycine-HCl, pH 1.5 at a flow rate of30 l/min. Kinetic parameters were determined using the kinetic functionof the BIAevalutation software (Biacore) with reference subtraction.Kinetic parameters for each antibody, ka (association rate constant), kd(dissociation rate constant) and K_(D) (equilibrium dissociationconstant) were determined.

Binding on Yeast Cell Surface

scFv constructs were expressed on the surface of yeast using the PCTCON2plasmid. Induced yeast were incubated with antigen for 1 hr at roomtemperature to reach equilibrium. Binding was then fixed by placing theyeast on ice, unbound antigen was washed away with ice cold PBS+0.1%BSA, and yeast were dual stained with anti-cmyc FITC [expression tag]and anti-6×HIS dylight 650 [antigen tag]. Fluorescence signal wasquantified by FACS and a binding curve was generated using a range ofantigen concentrations.

RVP Neutralization

A fixed volume of dengue reporter virus particles (RVP, IntegralMolecular) that yielded approximately 600,000 relative light units (RLU)was incubated with varying concentrations of antibody for 1 hour at 37°C. The strain of RVP was TVP360 (DV4). Antibody/RVP mixtures were thenapplied to 1.5×104 Vero cells pre-plated in 96-well plates withDulbecco's modified eagle medium (DMEM) supplemented with 10% fetalbovine serum, 1% non-essential amino acids, 2 mM L-Glutamine, 20 mMHEPES pH 8.0 and incubated for 72 hours at 37° C. Renilla luciferaselysis reagent (Promega) was added to each well and incubated for 30minutes at room temperature. Light output was measured using a BioTekSynergy 2 luminometer with direct injection of the renilla luciferasereagent. RLU data were normalized by RVP infection in the absence ofantibody (100% infection), and a four-parameter logistic equation wasfit to the data to determine EC50 values.

Results

Competition ELISA

Relative to 4E5A, several of the mutants exhibited higher affinitybinding to DENV-4 (defined as greater than 1.25), including VH_S26_del,VH_G27_del, and VH_G27A (FIG. 12). These mutants also exhibited higheraffinity binding to DENV-3.

Surface Plasmon Resonance

Consistent with the ELISA results, two of the mutants exhibited higheraffinity binding to DENV-4 (defined as greater than 1.25), includingVH_S26_del and VH_G27_del (FIG. 13B). These mutants also exhibitedslightly higher affinity binding to DENV-3. Binding to DENV-1 and -2(FIG. 13A) was unchanged.

Binding on Yeast Cell Surface

As a single chain Fv, VH_S26_del and VH_G27_del exhibited higheraffinity binding to DENV-4 (FIG. 14).

RVP Neutralization

VH_S26_del exhibited stronger neutralization of DENV-4 RVP, ˜19×, thatof 4E5A (FIG. 15). 4G2 is a control antibody used to standardize theassay.

REFERENCES

-   1. Friguet B, Chaffotte A F, Djavadi-Ohaniance L, Goldberg M E.    Measurements of the true affinity constant in solution of    antigen-antibody complexes by enzyme-linked immunosorbent assay.    Journal of Immunological Methods. 1985; 77(2):305-19.-   2. Martineau P. Affinity Measurements by Competition ELISA. In:    Kontermann R, Dubel S, editors. Antibody Engineering. Berlin:    Springer; 2010. p. 657-65.-   3. Bobrovnik S A. Determination of antibody affinity by ELISA.    Theory. Journal of Biochemical and Biophysical Methods. 2003;    57(3):213-36.

EQUIVALENTS AND SCOPE

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention, described herein. The scope of the presentinvention is not intended to be limited to the above Description, butrather is as set forth in the appended claims.

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process. Furthermore, it is to be understood that theinvention encompasses all variations, combinations, and permutations inwhich one or more limitations, elements, clauses, descriptive terms,etc., from one or more of the listed claims is introduced into anotherclaim. For example, any claim that is dependent on another claim can bemodified to include one or more limitations found in any other claimthat is dependent on the same base claim. Furthermore, where the claimsrecite a composition, it is to be understood that methods of using thecomposition for any of the purposes disclosed herein are included, andmethods of making the composition according to any of the methods ofmaking disclosed herein or other methods known in the art are included,unless otherwise indicated or unless it would be evident to one ofordinary skill in the art that a contradiction or inconsistency wouldarise.

Where elements are presented as lists, e.g., in Markush group format, itis to be understood that each subgroup of the elements is alsodisclosed, and any element(s) can be removed from the group. It shouldit be understood that, in general, where the invention, or aspects ofthe invention, is/are referred to as comprising particular elements,features, etc., certain embodiments of the invention or aspects of theinvention consist, or consist essentially of, such elements, features,etc. For purposes of simplicity those embodiments have not beenspecifically set forth in haec verba herein. It is noted that the term“comprising” is intended to be open and permits the inclusion ofadditional elements or steps.

Where ranges are given, endpoints are included. Furthermore, it is to beunderstood that unless otherwise indicated or otherwise evident from thecontext and understanding of one of ordinary skill in the art, valuesthat are expressed as ranges can assume any specific value or subrangewithin the stated ranges in different embodiments of the invention, tothe tenth of the unit of the lower limit of the range, unless thecontext clearly dictates otherwise.

In addition, it is to be understood that any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Since such embodiments aredeemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein.

The publications discussed above and throughout the text are providedsolely for their disclosure prior to the filing date of the presentapplication. Nothing herein is to be construed as an admission that theinventors are not entitled to antedate such disclosure by virtue ofprior disclosure.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. The scope of the presentinvention is not intended to be limited to the above Description, butrather is as set forth in the following claims:

1-26. (canceled)
 27. A cell line expressing an antibody agent accordingto claim
 40. 28-30. (canceled)
 31. A kit comprising: at least oneantibody agent according to claim 40; a syringe, needle, or applicatorfor administration of the at least one antibody or fragment to asubject; and instructions for use.
 32. A method of manufacturing apharmaceutical composition, the method comprising steps of: providing anantibody agent according to claim 40; and formulating the antibody agentwith at least one pharmaceutically acceptable carrier or excipient, sothat a pharmaceutical composition is generated. 33-38. (canceled)
 39. Anantibody agent comprising at least one antibody, which at least oneantibody comprises two heavy chains and two light chains, wherein: theheavy chain CDRs are identical to reference CDRs found between residues27 and 33, residues 53 and 58, and residues 100 and 106 of SEQ ID NO:29except that at least one of the heavy chain CDRs differs by a singleamino acid substitution relative to its reference CDR; and the lightchain CDRs are identical to reference CDRs found between residues 24 and38, residues 54 and 60, and residues 93 and 101 of SEQ ID NO:30, or atleast one of the light chain CDRs differs by a single amino acidsubstitution relative to its reference CDR, wherein the antibody agent:(i) competes with reference antibody 4E5A for binding to Dengue Virus;or (ii) binds to an epitope that is or comprises an amino acid sequencewithin: SEQ ID NO:17 (EDIII-DV1), SEQ ID NO:18 (EDIII-DV2), SEQ ID NO:19(EDIIIDV3), SEQ ID NO:20 (EDIII-DV4), or combinations thereof.
 40. Anantibody agent that: (a) has a heavy chain variable region that shows atleast 95% substantial sequence homology with that of heavy chainvariable region of 4E5A (SEQ ID NO. 29) and a light chain variableregion that shows at least 95% substantial sequence homology with thatof light chain variable region of 4E5A (SEQ ID NO. 30); and (b) itsheavy chain comprises one or more of the following mutations relative to4E5A: VH_S26_del; and VH_G27 del or VH_G27A.
 41. A method of treating asubject, the method comprising a step of: administering to a subjectsuffering from or susceptible to Dengue virus an antibody agentaccording to claim
 40. 42. A method of assessing an antibody agent that:(i) has a heavy chain variable region that shows at least 90%substantial sequence homology with that of heavy chain variable regionof 4E5A (SEQ ID NO. 29 and comprises one or more of the followingmutations relative to 4E5A: VH_S26_del; and VH_G27 del or VH_G27A; and(ii) has a light chain variable region that shows at least 90%substantial sequence homology with that of light chain variable regionof 4E5A (SEQ ID NO. 30); the method comprising steps of assessing if theantibody agent: (a) competes with 4E5A for binding to an epitope withineach of SEQ ID NO. 17 (EDIII-DV1), SEQ ID NO. 18 (EDIII-DV2), SEQ ID NO.19 (EDIII-DV3), SEQ ID NO. 20 (EDIII-DV4); (b) shows enhanced affinityfor the epitope within SEQ ID NO. 20 (EDIII-DV4) relative to that shownby 4E5A; and/or (c) shows comparable affinity to that shown by 4E5A forthe epitopes within each of SEQ ID NO. 17 (EDIII-DV1), SEQ ID NO. 18(EDIII-DV2), and SEQ ID NO. 19 (EDIII-DV3).
 43. The method of claim 42,wherein the step of assessing comprises determining ability of theantibody agent to bind to an epitope that is or comprises an amino acidsequence within: SEQ ID NO. 17 (EDIII-DV1), SEQ ID NO. 18 (EDIII-DV2),SEQ ID NO. 19 (EDIII-DV3), SEQ ID NO. 20 (EDIII-DV4), or combinationsthereof.
 44. The method of claim 43, wherein the step of determiningcomprises performing binding assays using a range of concentrations ofthe antibody agent and/or the epitope.
 45. A method of detectinginfluenza HA in a sample, the method comprising steps of: contacting thesample with an antibody agent of claim 40; and detecting binding of theantibody agent to HA in the sample.
 46. The method of claim 43 whereinthe sample is a biological sample
 47. The method of claim 43 wherein thesample is an environmental sample.